(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/226828 A2 13 December 2018 (13.12.2018) W !P O PCT

(51) International Patent Classification: OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, C07D 229/02 (2006.01) A61K 31/396 (2006.01) SC, SD, SE, SG, SK, SL, SM, ST, SV, SY,TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (21) International Application Number: PCT/US2018/036256 (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (22) International Filing Date: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, 06 June 2018 (06.06.2018) UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (25) Filing Language: English TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, (26) Publication Langi English MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (30) Priority Data: TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, 62/5 15,846 06 June 2017 (06.06.2017) KM, ML, MR, NE, SN, TD, TG). 62/628,372 09 February 2018 (09.02.2018) 62/65 1,599 02 April 2018 (02.04.2018) Published: — without international search report and to be republished (71) Applicant: PRESIDENT AND FELLOWS OF HAR¬ upon receipt of that report (Rule 48.2(g)) VARD COLLEGE [US/US]; 17 Quincy Street, Cam bridge, MA 02138 (US). (72) Inventors: WOO, Christina, M.; 84 Richdale Avenue, Unit 4, Cambridge, MA 02140 (US). GAO, Jinxu; 7 Perry Street Apt. 1, Somerville, MA 02143 (US). (74) Agent: BAKER, C , Hunter; Wolf, Greenfield & Sacks, P.C., 600 Atlantic Avenue, Boston, MA 02210-2206 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ,

(54) Title: DETERMINING SMALL MOLECULE-PROTEIN AND PROTEIN-PROTEIN INTERACTIONS

0 }Small molecule labeling [ J 2) Capture binding sites 3) Capture PP s

= H, nalid 4 } Enrichment and MB analysis R t - c probe Pr e linkage map mechanism of action

< Figure 1. oo ∞ (57) Abstract: Provided herein are methods, systems, kits, and compositions useful for determining small molecule-protein interactions and protein-protein interactions. The photo-click tags provided herein can be conjugated to a small molecule or amino acid analog to oo provide compounds that can be integrated into a protein through photo-conjugation, allowing for identification of a small molecule-pro tein interaction or protein-protein interaction to elucidate the small molecules mechamsm of action or the protein targeted by the small o molecule. In some embodiments, the photo-click tags comprise a photo-conjugation moiety and a click chemistry handle, allowing for the attachment of various functional groups (e.g., affinity tags) to the small molecule or amino acid analog. RELATED APPLICATIONS [0001] This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Applications, U.S. S.N. 62/515,846, filed June 6, 2017, U.S. S.N. 62/628,372, filed February 9, 2018, and U.S. S.N. 62/651,599, filed April 2, 2018, each of which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

[0002] Small molecule regulation of the proteome constitutes one of the oldest methods of therapy known to humankind. However, despite entering an era of target-based therapy and personalized medicine, parallel advances in understanding the precise molecular outcomes of small molecule therapeutics remain under-developed. Currently, the state of the art involves attachment of small molecules to affinity handles and immobilization on a solid support, followed by in vitro affinity purification. Alternatively, target-based dmg discovery evaluates the affinity of small molecules for a specific purified protein. These approaches fail to reveal the structural basis of the interaction (e.g., binding site), changes to protein-protein interactions (PPIs), and broader system-wide {e.g., proteome, interactome, or genome) effects. As a result, the vast majority of protein interactors are silently overlooked i current mechanism of action studies, leading to missed opportunities and incomplete toxicology profiles. [0003] The primary bottleneck is the lack of an approach to globally reveal proteomic interactions {e.g., protein-protein interactions (PPIs)) mediated by a small molecule. Protein- protein interactions are implicated in thousands of diseases, and thus it is imperative to understand both normal and abnormal PPIs. For example, this gap is particularly notable in the case of the immunomodulatory drugs (IMIDs), thalidomide, lenalidomide, and pomalidomide, a class of pluripotent therapeutics that lack a defined mechanism of action. These, as well as other, IMIDs have been the focus of extensive time-consuming mechanism of action studies, which have inspired popular conclusions about the importance of enantioselectivity in drug discovery due to their single stereocenter. However, the IMIDs are rapidly racemized and metabolized in plasma, making any attempt at characterizing the phenotype behind a specific isoform inconclusive. A complete understanding of the role of M D isoforms {e.g., R-lenalidomide versus S-lenalidomide) demands a molecular approach. A method to directly map the small molecule interactome has the potential to accelerate drug discovery by providing structural insight and instant validation of the binding interaction between a small molecule and its one or more target proteins, yet such global characterization is rarely performed due to the under-developed state of the current technology.

SUMMARY OF THE INVENTION [0004] The present disclosure provides, in some aspects, compositions, techniques, methods, systems, and kits capable of mapping the direct and indirect effects of small molecules within the proteome. Some aspects of the present disclosure provide a small photo-click tag that enables efficient capture, enrichment, and characterization of small molecule binding sites on proteins. These small photo-click chemical tags can be incorporated into a variety of small molecules, including small molecule drugs, such as immunomodulatory drugs (e.g., ienalidomide, thalidomide, and pomalidomide) and non-steroidal anti-inflammatory drugs (NSAIDs) (e.g., naproxen, celecoxib, and indomethacin). The small size of these photo-click chemical tags ensures that small molecule binding does not perturb the native small molecule- or protein-protein interactions. After treatment of the whole cell proteome with the photo-click modified small molecule, the resulting interactions (e.g., small molecule-protein or protein-protein interactions) are captured (i.e., "frozen" in place) (see, e.g., Figure 7 and Figure 8) . These interactions can be affinity enriched for characterization, for example, by mass spectrometry (MS) (e.g., mass-independent or isotope-targeted mass spectrometry). In addition to revealing the binding site of the small molecule, thus helping to elucidate its mechanism of action, the photo-click modified small molecules can also be used to reveal downstream effects of the small molecule on cellular pathways by mapping protein-protein interactions (see, e.g., Figure J). In addition to confirming mechanisms of action of small molecules through their interaction with known target proteins, this approach can be used to identify transient complexes formed with previously unidentified target proteins. This technique is typically referred to throughout the present disclosure as Small Molecule Interactome Mapping by Photo-Affinity Labeling (SIM-PAL), or Minimally-Interfering Photo-Affinity Labeling (MI-PAL) when the smallest exemplified photo-click chemical tags provided herein are employed. The binding site identification method provided by SIM-PAL and MI-PAL is a strategy capable of precisely defining binding preferences between enantiomers and metabolites of a small molecule of interest. Additionally, amino acid analogs comprising a photo-click tag enable the measurement of protein-protein interaction (PPI) perturbations in the presence of the small molecule of interest, allowing for the determination of a global "interactome" in the presence of the small molecule (e.g., drug). [0005] Thus, in one aspect, the present disclosure provides photo-click tags that are readily incorporated into a small molecule scaffold. In general, the multi-functional photo-click tags comprise two functional moieties: a photo-conjugation moiety that can covalently capture the protein target (e.g., an enzyme that binds to a small molecule of interest, a receptor, an antibody, etc.), and a biocompatible handle (e.g., a click chemistry handle) for functionaiization with a reporter molecule or affinity tag (e.g., a biotinylated affinity tag). In some embodiments, the photo-click tag compri ses (a) a photo-conjugation moiety, and (b) a click chemistry handle. In some embodiments, the photo-conjugation moiety is a diazirine moiety. In some embodiments, the photo-click tag comprises (a) a diazirine moiety and (b) a click chemistry handle. In some embodiments, the click chemistry handle is an alkyne. In some embodiments, the photo-click tag comprises (a) a diazirine moiety and (b) an alkyne. In some embodiments, the photo-conjugation moiety forms a reactive species upon irradiation with light (i.e., forms an activated photo-click tag). In some embodiments, the diazirine forms a reactive carbene species upon irradiation with light. In some embodiments, the light has a wavelength of between about 10 nm and 400 nm. In some embodiments, the reactive species reacts with a C-C, C-H, N-H, or O-H bond of a protein. In some embodiments, a new covalent bond is formed between the activated photo-click tag and the protein. )6] In some embodiments, the photo-click tag comprises the structure:

wherein Y, M. X, n, and m are as defined herein.

7] In some embodiments, the photo-click tag is of the formula: [0008] In another aspect, the present disclosure provides compounds that are covaiently linked to any of the photo-click tags provided herein {i.e., photo-click conjugated compounds). In some embodiments, the compound is of Formula (I):

wherein S is a small molecule, P is a photo-click tag, and L is a linker, as provided herein. [0009] In some embodiments, L comprises an ester, an ether, an amine, or an amide. [0010] In some embodiments, S is an antibiotic, an anti-proliferative agent, an anti-cancer agent, a chemotherapeutic agent, an anti-angiogenesis agent, an anti-inflammatory agent, an immunosuppressant, an immunomodulatory agent, an anti-bacterial agent, an anti-viral agent, a cardiovascular agent, a cholesterol-lowering agent, an anti-diabetic agent, an anti-allergic agent, a contraceptive agent, or a pain-relieving agent. In some embodiments, S is an anti¬ inflammatory agent, or derivative thereof. In some embodiments, S is an immunomodulatory agent, or derivative thereof. In some embodiments, S is a chemotherapeutic agent, or derivative thereof. [0011] In some embodiments, S is a steroid, or derivative thereof. [0012] In some embodiments, the compound comprises one or more isotopically labeled atoms. In some embodiments, the isotopically labeled atom is N, l C, yF, or H . [0013] In yet another aspect, provided herein are methods for using the photo-click tags and compounds conjugated to photo-click tags provided herein to determine, analyze, and evaluate small molecule-protein or protein-protein interactions. In some embodiments, the proteins are present in a cell, allowing for the determination of these interactions in the native cellular environment. [0014] In one aspect, provided herein is a method for identifying a target protein of a small molecule. In some embodiments, the method comprises: (i) providing a compound comprising the small molecule connected to a photo-click tag via a linker, wherein the photo- click tag comprises (a) a diazirine moiety, and (b) a click chemistn,' handle; (ii) activating the diazinne moiety by irradiating the compound of (i) with a specific wavelength of light, (iii) contacting the target protein with the activated compound of (ii); (iv) forming a complex through a photo-induced covalent bond between the activated compound of (ii) and the protein; and (v) identifying the complex produced in (iv) that is bound to the compound, thereby identifying the target protein of the small molecule. [0015] In another aspect, provided herein is a method for identifying the binding site of a small molecule on a protein. In some embodiments, the method comprises (i) providing a compound comprising the small molecule connected to a photo-click tag via a linker, wherein the photo-click tag comprises (a) a diazirine moiety, and (b) a click chemistry handle; (ii) activating the diazirine moiety by irradiating the compound of (i) with a specific wavelength of light; (iii) contacting the protein with the activated compound of (ii); (iv) forming a complex through a photo-induced covalent bond between the activated compound of (ii) and the protein; (v) digesting the protein of the complex into constitutive peptides in the presence of a protease; and (vi) identifying the one or more peptides produced in (iv) that is bound to the compound, thereby identifying the protein binding site of the small molecule. [0016] In another aspect, provided herein is a method for identifying an interaction between a first protein and a second protein in a cell. In some embodiments, the method comprises: (i) providing the cell with an amino acid analog, wherein the amino acid analog comprises a photo-click tag comprising (a) a diazirine moiety, and (b) a click chemistry handle, and wherein the amino acid analog is incorporated into the first protein and/or the second protein during protein synthesis, (ii) activating the diazirine moiety of t e amino acid analog by irradiating the cell with a specific wavelength of light; (iii) contacting the first protein or the second protein with the activated compound of (ii); (iv) forming a protein-protein complex through a photo-induced covalent bond between the activated amino acid analog of the first protein and an amino acid in the second protein; and (v) identifying the complex produced in (ii) that comprises the amino acid analog covalently linking the first protein and the second protein, thereby identifying the first protein and the second protein involved in the interaction. [0017] Also provided herein are kits comprising any of the photo-click tags or photo-click tagged compounds provided herein. In addition, also provided herein are kits for use in performing any of the methods provided herein. [0018] The summary above is meant to illustrate, in a non-limiting manner, some of the embodiments, advantages, features, and uses of the technology disclosed herein. Other embodiments, advantages, features, and uses of the technology disclosed herein will be apparent from the Detailed Description, the Drawings, the Examples, and the Claims.

BRIEF DESCRIPTION OF THE DRAWINGS [0019] The accompanying drawings, which constitute a part of this specification, illustrate several exemplary embodiments of the invention and together with the description, serve to explain certain principles of the invention. The embodiments disclosed in the drawings are exemplar}' and do not limit the scope of this disclosure. [0020] Figure 1 is a generalized, non-limiting schematic showing how direct and indirect effects of a small molecule (lenalidomide is exemplified) on the whole cell proteome can be studied using the technology disclosed herein, such as SIM-PAL and MI-PAL. [0021] Figure 2 is a generalized, non-limiting schematic outlining the MI-PAL global binding site mapping strategy. [0022] Figure 3 shows immunomodulatory drugs (IMIDs) as a non-limiting example to illustrate the importance of chirality in drug discovery. Despite this, the current mechanism of action of these IMIDs, for example, lenalidomide, remains incomplete and demands elucidation by a molecular approach, such as SIM-PAL or MI-PAL [0023] Figures 4A-4C shows a general schematic summarizing the gap in current technologies for analyzing small molecule-protein or protein-protein interactions. Figure 4A illustrates the types of changes induced by small molecule binding to a target protein. Figure 4B summarizes the current state of the dmggable proteome, with a particular focus on the large percentage of the dmggable proteome that is characterized as "understudied " Adapted from Griffith et al. (2013) DGIdb: mining the dmggable genome. Nature Methods 10, 1209- 1210. Figure 4C shows the predicted impact of technologies, such as SIM-PAL or MI-PAL as described herein, in uncovering dmggable interactions that are currently considered "understudied" due to the lack of capable technology SIM-PAL and MI-PAL represent strategies that are broadly translatable to any small molecule of interest. [0024] Figure 5 shows a generalized, non-limiting schematic outlining the SIM-PAL global binding site mapping strategy. [0025] Figures 6A-6B shows a generalized strategy for developing photo-click conjugated small molecules {e.g., lenalidomide) as mechanistic probes. Figure 6A shows examples of minimally interfering photo-click probes that have been developed herein, along with the current standard for photo-click probes (See, Li et al. (201 3) Design and Synthesis of Minimalist Terminal Alkyne-Containing Diazirine Photo-Crosslinkers and Their Incorporation into Kinase Inhibitors for Cell- and Tissue-Based Proteome Profiling. Agnew Chem h t FA, 52, pp. 8551-8556). These smaller photo-click tags may lead to less perturbation of the small molecule and/or protein binding target, have superior photo- crosslinking properties, and/or have superior click chemistry rates compared to the current, larger photo-click probes. Figure 6B shows improved copper (I)-catalyzed alkyne-azide cycloaddition (CuAAC) properties of the minimally interfering, electronically tuned "MI- PAL" photo-click tag. Asterisks (*) indicate isotopically labeled atoms. [0026] Figure 7 shows a generalized strategy for applying the minimally-interfering "MI- PAL" photo-click tag to map small molecule binding sites in the whole multiple myeloma cell proteome. These results show that the binding and interactions of R- versus S- enantiomers can be elucidated using the SIM-PAL or MI-PAL technique described herein. [0027] Figure 8 shows a generalized, non-limiting schematic to study the effect on downstream protein-protein interactions in the presence of a small molecule (e.g., lenalidomide) or combination therapy. This method uses a photo-click labeled amino acid derivative to capture {e.g., "freeze") and identify protein-protein interactions, allowing for the generation of a proteome linkage map. [0028] Figure 9 shows a generalized, non-limiting schematic outlining the SIM-PAL global binding site mapping strategy using exemplary photo-click probes. See, e.g., Flaxman HA and oo CM (2017) Mapping the Small Molecule Interactome by Mass Spectrometry. Biochemistry, 57(2), pp. 186-193. [0029] Figure 10 shows a generalized, non-limiting schematic outlining system-level binding and pathway analysis in the presence of a small molecule of interest, such as a drug or drug candidate. SIM-PAL analysis can be used to predict new drug targets {i.e., proteins) or aid in the optimization of existing candidate molecules based on information, such as binding affinity, binding site size, and binding site conformation, given by the SIM-PAL analysis. [0030] Figure 11 shows potential, non-limiting applications of the SIM-PAL or MI-PAL technology. This technology can be used to discover and engineer molecular interactions {e.g., small molecule-protein interactions). [0031] Figures 12A-12C show a general strategy to profile the NSA D interactome using SIM-PAL. Figure 12A outlines the process in which photo-NSAIDs are applied in vivo (i.e., in celluio) and conjugated to protein binding partners by photo-irradiation. Conjugated proteins are tagged by probe 10 using copper (I)-catalyzed alkyne-azide cycloaddition (CuAAC) and enriched to separately obtain the protein interactome and conjugated peptides representing binding site hotspots. Conjugated peptides are analyzed by isotope-targeted mass spectrometry (MS). Figure 12B shows stmctures of NSAIDs naproxen (1), celecoxib (2), and indomethacin (3), their photo-NS AID analogs 4-6, and the negative controls tag 7,

the orthogonal compound photo-glutarimide 8, and the celecoxib analog 9 . COX-2 IC50 by ELISA is shown below each structure. Figure 12C shows the structure of the cleavable biotin azide probe 10. Probe 10 is prepared as a 1:3 mixture of stable C :1 C isotopes (highlighted in red). [0032] Figures 13A-13E show a comparative analysis of NSAIDs and photo-NSAIDs with recombinant COX-2. Figure 13A shows a fluorescence image of photo-NSAID binding to COX-2 and competitive displacement by the respective NSA1D. COX-2 (125 ng) was incubated with photo-NSAIDS with or without the parent molecule, photo-crosslinked, and clicked with TAMRA-azide. Figure 13B shows the docking structure of photonaproxen (4, red) and naproxen (1, blue) with COX-2. Figure 13C shows the docking structure of photo- celecoxib (5, green) and celecoxib (2, blue) with COX-2. Figure 3D shows the docking staicture of photo-indomethacin (6, yellow) and indomethacin (3, blue). Figure J3E shows the docking structure of diazirine tag 7 (purple) with COX-2. White box indicates part of

COX-2 that is enlarged in sections 13B-13D. COX-2 ( 1 g) was separately conjugated to each of the photo-NS AIDs (10 µΜ) or the diazirine tag 7 (10 µΜ), tryptically digested, and analyzed on an Orbitrap Elite. Conjugated peptides observed by MS are highlighted for each photo-NSAID. Docking structures were either the lowest desolvation energy or highest interface area size binding models created by Patchdock (October, 2017) Structure of COX-2 from PDB: 5KIR. [0033] Figures 14A-14E sho the photo-NSAID (250 µΜ) protein interactome. Figure 14A shows protein enrichment of the photo-NSAIDs against the tag 7 based on PSMs. Proteins that were not statistically significant across the two biological replicates are displayed at a fold change of zero. Figure 14B shows the overlap across the Jurkat photo-NSAID enriched proteome. Figure 14C shows proteomic overlap between enriched proteins from Jurkat and K562 cells. Figure 14D shows sub-cellular localization of the 1034 enriched proteins. Figure 14E shows selected protein interaction networks captured by photo- NSAIDs Color scheme: red = significantly enriched; pink = greater than 2-fold enriched; grey = identified in data; white = member of the protein complex not identified in data. Dashed border indicates direct observation of at least one conjugated peptide. Protein interaction networks were built using The Comprehensive Resource of Mammalian Protein Complexes (CORUM) as a reference. Half maximal effective concentration (EC50) values for inhibition of the NF-κΒ pathway as determined by a NF-κΒ luciferase reporter described in Example [0034] Figures 15A-15E show the evaluation of photo-NSAID binding site hotspots identified by SIM-PAL. Figure ISA shows precursor pattern distribution (MSI) and database assignment (MS2) for a histone H2A peptide conjugated to each of the photo-NSAIDs. Figure JSB shows a cluster diagram of histone protein complexes with at least one observed binding site to a photo-NSAID. High confidence interactions between two clusters made using STRING Figure 15C shows the structure of the nucleosome (PDB: 2CV5). Peptides from histone H2A (red) and histone H2B (blue) that were conjugated by all three photo- NSAIDs are highlighted. Figure 151) shows competitive displacement of photo-NSAIDs by the parent compound. Jurkat cell iysates conjugated to the indicated compound with or without the parent compound were clicked with the biotin probe 10, captured on streptavidin-agarose, and probed for histone H2A, H2B, Ku70, NPM1, or NF-κΒ p65. Figure 15E shows a cellular thermal shift assay performed on Jurkat cells in the presence of the indicated compound, probed for histone H2A. [0035] Figures 16A-16D show inhibition of COX-2 by (Figure 16A) photo-naproxen (4) and

naproxen (1), Figure 16B) photo-celecoxib (5) and celecoxib (2), and (Figure 16 ) photo- indomethacin (6) and indomethacin (3). Figure 16D shows COX-2 ICso values for photo- NSAIDs and NSAIDs. ICso values were determined as described by the ELISA-based COX-2 inhibitor screening assay and performed in triplicate. Data is representative of two biological replicates. [0036] Figures 17A-17D show MTT cell viability assay for photo-NSAIDs and NSAIDs in Jurkat cells. Dose-response curves for (Figure 17A) photo-naproxen (4) and naproxen (1),

(Figure 17B) celecoxib (2), photo-celecoxib (5) and celecoxib analog 9, and (Figure 17C

photo-indomethacin (6) and indomethacin (3). Figure 17D shows IC50 values for NSAIDs and photo-NSAIDs in Jurkat cells. All dose-response curves were obtained in triplicate. [0037] Figures 18A-18C show photo-NSAID dose-dependence and photo-irradiation- dependent labeling of Jurkat proteins. Figure 18A shows dose-dependent labeling of Jurkat cells with the photo-NSAIDs, the tag 7, or photo-glutarimide 8 . Jurkat cells were incubated with the small molecule at the indicated concentration for I hour at 37 °C and photoirradiated (30 minutes, 4 °C). Irradiated cells were lysed, clicked with tetramethylrhodamine-azide (TAMRA-azide), and visualized on gel. Coomassie blue staining shows equal protein loading. Figure 18B shows anti-biotin Western blot from 250 µΜ of photo-NSAID or DMSO

control treated Jurkat cells with (+) or without (-) UV irradiation for photo-naproxen (4),

photo-celecoxib (5), and photo-indomethacin (6). Ponceau S staining shows equal amount of protein loading. Figure 18C shows competition assay titration with photo-celecoxib (5) and

the competitor celecoxib (2) at 1:1, 1:10, and 1:100 molar ratios. Jurkat cells were incubated with the tag 7, photo-celecoxib (5), or co-treated with photo-celecoxib (5) and the parent

compound celecoxib (2) at : , 1: 0, and 1: 00 molar ratios for I hour at 37 °C, followed by

photoirradiation (30 minutes, 4 °C) and cell lysis. Cell Iysates were adjusted to 1.5 mg/mL, and were then clicked with 200 µΜ biotin azide probe 10, 300 µΜ copper (II) sulfate, 600 µΜ BTTP, and 2.5 mM freshly-prepared sodium ascorbate for 2 hours at 24 °C with rotation, followed by analysis by Western blotting using HRP-streptavidin conjugate. Ponceau S staining shows equal amount of protein loading. [0038] Figure 19 shows an anti-biotin Western blot for enriched small molecule conjugated proteins from Jurkat cells. Jurkat cells were treated with a photo-NSAID or the tag 7, photo- irradiated and clicked with the cleavable biotin azide probe 10 (click). Biotinylated proteins were enriched on streptavidin-agarose beads, and the beads were washed (1% RapiGest, 6M urea, PBS). The biotin-depleted whole proteome (supernatant) and the beads (capture) were analyzed by gel. Ponceau S staining shows protein loading. [0039] Figures 20A-20C show photo-NSAID interactions with COX-2 in Jurkat cells. Figure

2OA shows a Western blot probed for COX-2 of photo-NSAID captured proteins and competitive displacement by the parent compound in Jurkat whole cell lysates. Jurkat cells were incubated with photo-NSAIDs [250 µΜ of photo-naproxen (4) and photoindomethacin

(6); 50 µΜ of photo-celecoxib (5)] in the presence or absence of the parent compound (1:10 molar ratio) for 2 hours and photo-irradiated. Photo-irradiated proteins were iysed and clicked with the biotin azide probe 10 (load) and enriched on streptavidin-agarose (capture). Figure 20B shows a cellular thermal shift assay probed for COX-2 in Jurkat cells i the presence of 50 uM of the tag 7, the celecoxib analog 9, celecoxib (2), or photo-celecoxib (5). Data are representative of two independent biological replicates. Figure 20C shows quantification of COX-2 signal in cellular thermal shift assay using ImageJ and GraphPad Prism software. The solid lines represent the best fits of the data to the Boltzmann sigmoid equation, resulting in an apparent Tagg of 27.6 ± 0.6 °C for the tag 7, and 40.9 ± .0 °C for the celecoxib analog 9, whereas both celecoxib (2) and photo-celecoxib (5) stabilized COX-2 at 50.5 ± 0 6 °C and 52.2 ± 1.0 °C, respectively. [0040] Figures 21A-21C show proteomics data reproducibility and protein overlap of analyzed compounds. Figure 21A shows relative protein abundance using peptide spectral matching (PSM) based label free quantification across the two Jurkat biological replicates collected at 250 µΜ photo-NS AIDs. figure 2113 shows the overlap across one biological replicate of the Jurkat photo-NSAID enriched proteome at 50 µΜ photo-NSAIDs. Figure 21C shows the proteomic overlap between enriched proteins from Jurkat cells exposed to 50 µΜ photo-celecoxib (5) or the celecoxib analog 9 . [0041] Figure 22 shows an anti-biotin Western blot for enriched small molecule conjugated proteins from K562 cells. K562 cells were treated with a photo-NSAID or the tag 7, photo- irradiated and clicked with the cleavable biotin azide probe 10 (click). Biotinylated proteins were enriched on streptavidin-agarose beads, and the beads were washed (1% RapiGest, 6 M urea, PBS). The biotin-depieted whole proteome (supernatant) and the beads (capture) were analyzed by gel. Ponceau S staining shows protein loading. [0042] Figure 23 shows a verm diagram of statistically-enriched photo-NSAID (250 µΜ ) protein interactome from K562 cells across two biological replicates.

[0043] Figure 24 shows a TNF-a titration curve for NF-KB-RE -1UC2P HEK293 cells treated with 5 µΜ of the tag 7, ceiecoxib (2), photo-celecoxib (5), and DMSO. The luminescence was quantified using the O E-G o Luciferase Assay System Reagent on a microplate reader FilterMax F3. All data were obtained in triplicate, data representative of two independent experiments. [0044] Figure 25 shows example spectra of photo-naproxen (4) and photo-celecoxib (5) conjugated to a peptide from histone H2B. Spectra were validated for isotopic pattern (MSI) and spectral assignment (MS2) by SEQUEST HT. [0045] Figure 26 shows a synthetic scheme for the synthesis of photo-NSAID analogs. Reagents and reaction conditions: (a) (i) HBr, 12 hours, reflux (ii) acetyl chloride, CH OH, 4 hours, reflux (95%, two steps); (b) K2CO3, S7, DMF, 12 hours, 24 °C (85%); (c) 1M NaOH, methanol, 4 hours, 24 °C (98%), (d) S8, ethanol, 12 hours, reflux (99%); (e) K2CO3, S7,

DMF, 12 h, 24 C (75%); (f) N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC), triethyl amine, S6, DMAP, DMF, 12 hours, 24 °C (88%); (g) GDI,

THF, 12 hours, 24 °C (95%); (h) 3-aminopiperidine-2,6-dione hydrochloride, DBU, DMF, 12 hours, 24 °C (86%); (i) phenylhydrazine, ethanol, 12 hours, reflux (92%); (j) K2CO3, S7, DMF, 12 hours, 24 °C (68%). [0046] Figure 27 shows a synthetic scheme for the synthesis of the cleavable biotin azide probe 10.

[0047] Figure 28 shows structures of arylalkyne 1, "minimalist" tag 2, and MI-PAL (3), chemical tags that possess a diazirine functional group and aikyne reporter handle. Retrosynthesis of 3 proceeds through the ester 4 and aikyne 5 . [0048] Figure 29 shows the synthetic scheme used for the synthesis of MI-PAL (3) from the ester 4 and the aikyne 5 . [0049] Figures 30A-C show photo-conjugation and CuAAC with MI-PAL (3) to the proteome. Figure 3 A shows photoconjugation of MI-PAL (3) to alpha-crystallin. Figure 30B shows an example collision-induced dissociation (CID) mass spectra of a peptide from alpha-crystaflin conjugated to MI-PAL (3). M represents the precursor mass. Figure 30C shows visualizion by Western blot of whole cell lysates from MM. I S (multiple myeloma) or K562 (chronic mylogenous leukemia) incubated with MI-PAL (3) and photoirradiated. Photoconjugated lysates were treated with biotin-azide and visualized by Western blot.

[0050J Figure 31 shows the synthetic scheme used for the synthesis of the MI-PAL-tagged glycine methyiester 12, the MI-PAL-tagged daunorubicin 13, and the MI-PAL-tagged mitomycin 14. [0051] Figure 32 shows the synthetic scheme used for the synthesis of the MI-PAL-tagged naproxen analog 16 and the MI-PAL-tagged β-estradiol 17 from the iodide 15.

DEFINITIONS [0052] Descriptions and certain information relating to various terms used i the present disclosure are collected herein for convenience. [0053] As used herein and i the claims, the singular forms "a," "an," and "the" include the singular and the plural reference unless the context clearly indicates otherwise. Thus, for example, a reference to "an agent" includes a single agent and a plurality of such agents. [0054] The term "agent" is used herein to refer to any substance, compound {e.g., small molecule, peptide, protein, nucleic acid), supramolecular complex, material, or combination or mixture thereof. A compound may be any agent that can be represented by a chemical formula, chemical structure, or sequence. Examples of agents include, e.g. , small molecules, polypeptides, nucleic acids {e.g., RNAi agents, antisense oligonucleotide, aptamers), lipids, polysaccharides, etc. In general, agents may be obtained using any suitable method known in the art. In some embodiments, the agent is a small molecule. In some embodiments, the agent is an antibiotic, anti-proliferative agent, an anti-cancer agent, a chemotherapeutic agent, anti- angiogenesis agent, anti-inflammatory agent, immunosuppressant, immunomodulatory agent, anti -bacterial agent, anti-viral agent, cardiovascular agent, cholesterol-lowering agent, anti diabetic agent, anti-allergic agent, contraceptive agent, or pain-relieving agent. In some embodiments, the agent is an anti-inflammatory agent. In some embodiments, the agent is an immunomodulatory drug. In some embodiments, the agent is a chemotherapeutic agent. These compounds may be conjugated to a photo-click tag provided herein. The ordinary skilled artisan will select an appropriate method for preparing a "photo-click conjugated agent" based, e.g., on the nature of the agent {e.g., the functional groups present in the agent) and the desired photo-click tag to be used. Examples of synthetic procedures for generating photo-click conjugated agents is provided in Examples 1 and 2 (also see Figures 26, 31, and 32). An agent may be at least partly purified. In some embodiments, an agent may be provided as part of a composition, which may contain, e.g., a counter-ion, aqueous or non aqueous diluent or carrier, buffer, preservative, or other ingredient, in addition to the agent, in various embodiments. In some embodiments, an agent may be provided as a salt, ester, hydrate, or solvate. In some embodiments an agent is cel -permeable, e.g., within the range of typical agents that are taken up by cells and acts intracellularly, e.g., within mammalian cells, to produce a biological effect. Certain compounds may exist in particular geometric or stereoisomeric forms. Such compounds, including cis- and traws-isomers, E- and Z-isomers, R- and S-enantiomers, diastereomers, (D)-isomers, (L)-isomers, (-)- and (+)-isomers, racemic mixtures thereof, and other mixtures thereof are encompassed by this disclosure in various embodiments unless otherwise indicated. Certain compounds may exist in a variety or protonation states, may have a variety of configurations, may exist as solvates {e.g., with water (i.e., hydrates) or common solvents) and/or may have different crystalline forms (e.g., polymorphs) or different tautomeric forms. Embodiments exhibiting such alternative protonation states, configurations, solvates, and forms are encompassed by the present disclosure where applicable. [0055] The term "amide," as used herein, refers to the group -C(=0)N(R X 1)-, wherein each RX is independently hydrogen; halogen; substituted or unsubstituted hydroxy!; substituted or unsubstituted thiol; substituted or unsubstituted amino; substituted or unsubstituted acyl, cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched alkyl; cyclic or acyclic, substituted or unsubstituted, branched or unbranched alkenyl; substituted or unsubstituted a!kynyl; substituted or unsubstituted aryl, substituted or unsubstituted heteroary!, aliphaticoxy, heteroaliphaticoxy, a y oxy, heteroalkyloxy, aryloxy, heteroaryloxy, aliphaticthioxy, heteroaliphaticthioxy, aikyithioxy, heteroalkylthioxy, arylthioxy, heteroarylthioxy, mono- or di- aliphaticamino, mono- or di- heteroaliphaticamino, mono- or di- alkylamino, mono- or di- heteroalkylamino, mono- or di-arylamino, or mono- or di- heteroarylamino. In some embodiments, RX s hydrogen. In some embodiments, a photo- click tagged compound herein comprises a small molecule covaiently linked to a photo-click tag by an amide. X, X [0056] The term "amine," as used herein, refers to the group -N(R )2- wherein each R is independently hydrogen; halogen; substituted or unsubstituted hydroxyl; substituted or unsubstituted thiol; substituted or unsubstituted amino; substituted or unsubstituted acyl, cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched a ky ; cyclic or acyclic, substituted or unsubstituted, branched or unbranched alkenyl; substituted or unsubstituted alkynyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, aliphaticoxy, heteroaliphaticoxy, alkyloxy, heteroalkyloxy, aryioxy, heteroaryl oxy, aliphaticthioxy, heteroaliphaticthioxy, alkylthioxy, heteroalkylthioxy, arylthioxy, heteroarylthioxy, mono- or di- aliphaticamino, mono- or di- heteroaliphaticamino, mono- or

di~ alkylamino, mono- or di- heteroalkylamino, mono- or di-arylamino, or mono- or di- heteroarylamino. In some embodiments, R is hydrogen. In some embodiments, a photo- click tagged compound herein comprises a small molecule covalently linked to a photo-click tag by an amine.

[0057] The term "anti-inflammatory agent" refers to any compound (e.g. small molecule) that exhibits anti-inflammatory properties when administered to a subject in need thereof. The anti-inflammatory agent may be a steroidal anti-inflammatory agent or a nonsteroidal anti-inflammatory agent. In some embodiments, the anti-inflammatory agent is a nonsteroidal anti-inflammatory drug. The term "nonsteroidal anti-inflammatory drug" or "NSAID" as

used herein refers to any compound (e.g., small-molecule) that can be classified as an NSAID. In general, an NSAID is a small molecule that reduces pain, reduces fever, prevents blood clots, and/or decreases inflammation, and the like. In general, NSAIDs work by inhibiting the activity of cyclooxygenase enzymes (COX-1 and/or COX-2). In cells, these enzymes are involved in the synthesis of key biological mediators, namely prostaglandins, which are involved in inflammation, and thromboxanes, which are involved in blood clotting. There are two types of NSAIDs available: non-selective and COX-2 selective. Non-selective NSAIDs inhibit the activity of both COX-1 and COX-2 In some embodiments, the anti inflammatory agent is a steroidal anti-inflammatory agent. The term "steroidal anti inflammatory agent" refers to any natural or synthetic agent that comprises the core structure of a steroid and exhibits an anti-inflammatory property when administered to a subject in need thereof. [0058] In some embodiments, the reaction used to generate a photo-click conjugated agent is a click chemistry reaction. In some embodiments, the reaction used to conjugate the photo- click conjugated agent to a target protein is a click chemistry reaction. In some embodiments, the reaction used to conjugate (i.e., "click") a label onto the photo-click tag is a click chemistry reaction. It is to be understood that any "click chemistry" reaction known in the art can be used to this end. Click chemistry is a chemical philosophy introduced by Sharpless in 2001 and describes chemistry tailored to generate substances quickly and reliably by joining small units together. See, e.g., Kolb, Finn, and Sharpless, Angew Chem Int Ed (2001) 40: 2004-2021; Evans, Australian Journal of Chemistry (2007) 60: 384-395. The term "click chemistry" does not refer to a specific reaction or set of reaction conditions, but instead refers to a class of reactions {e.g., coupling reactions). Exemplary coupling reactions (some of which may be classified as "click chemistry") include, but are not limited to, formation of esters, thioesters, amides e.g., such as peptide coupling) from activated acids or acyl halides; nucleophilic displacement reactions {e.g., such as nucleophilic displacement of a halide or ring opening of strained ring systems); azide-alkyne Huisgen cycloaddition; thiol-yne addition; imine formation; and Michael additions {e.g., maleimide addition). Examples of click chemistry reactions can be found in, e.g., Kolb, H . C ; Finn, M . G . and Sharpless, K . B . Angew. Chem. Int. Ed. 2001, 40, 2004-2021. Kolb, H . C . and Sharpless, K . B . Drug Disc. Today, 2003, 8, 112-1 137; Rostovtsev, V. V.; Green L . G ; Fokin, V. V. and Sharpless, K . B. Angew. Chem. Int. Ed. 2002, 41, 2596-2599; Tomoe, C . W.; Christensen, C . and Meldai, M . J. Org. Chem 2002, 67, 3057-3064 Wang, Q . et al. J. Am. Chem. Soc 2003, 125, 3192- 3193; Lee, L . V. et al. J. Am. Chem. Soc. 2003 125, 9588-9589; Lewis, W . G . et al Angew. Chem. Int. Ed. 2002, 41, 1053- 41057, Manetsch, R . etal, J. Am. Chem. Soc. 2004, 126, 12809- 12818; Mocharla, V. P. etal. Angew. Chem., Int. Ed. 2005, 44, 116-120; each of which is incorporated by reference herein. In some embodiments, the click chemistry reaction involves a reaction with an alkyne moiety comprising a carbon-carbon triple bond {i.e., an alkyne handle). In some embodiments, the click chemistry reaction is a copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. A CuAAC reaction generates a 1,4- disubstituted-l,2,3-triazole product {i.e., a 5-membered heterocyclic ring). See, e.g., Hein JE and Fokin VV (2010) Copper-catalyzed azide-alkyne cycloaddition (CuAAC) and beyond: new reactivity of copper (I) acetylides. Chem Soc Rev, 39(4), pp. 1302-13 15; the contents of which s incorporated by reference herein. For example, as shown in Examples 1 and 2, a label (e.g., a biotinylated affinity label) comprising an azide moiety can be conjugated to a photo-click tag comprising an alkyne using a CuAAC reaction. In some embodiments, the click chemistry reaction is a photo-click reaction. As used herein, a "photo-click" reaction is a reaction in which a compound is activated upon irradiation with a specific wavelength of UV light {i.e., between about 10 nm and about 400 nm). The activated compound can then rapidly form a covalent bond with the nearest target molecule {e.g., chemical bonds present in a protein). In some embodiments, the compound comprises a diazirine, which forms a reactive carbene upon irradiation with UV light. The activated carbene can then react with a nearby C-C, C-H, N-H, O-H, or X-H (X=heteroatom) bond present in a protein, thus conjugating the diazirine to the protein. See, e.g., Dubnisky L et al (201 ) Diazirine based photoaffinity labeling. Bioorg Med Chem 20, 554-570; which is incorporated herein by reference. The use of diazirines as photo-reactive crosslinking reagents, or photo-click reagents, has been described in, e.g., Sinz A . (2007) Investigation of Protein-Li gand

Interactions by Mass Spectrometry. Chem Med Chem, 2, pp. 425-43 , and Brunner J . (1993) New photoiabeling and crosslinking methods Am Rev Biochem, 62, pp. 483-514; the entire contents of each of which are incorporated herein by reference [0059] The term "compound" as used herein encompasses any small molecule, peptide, nucleic acid, protein, or derivative thereof that can bind to and/or modulate (e.g., increase the activity of, decrease the activity of) a target of interest (e.g., a protein, e.g., an enzyme, receptor, reporter protein, etc.)). In some embodiments, the compound is a small molecule. [0060] The term "ester," as used herein, refers to the group -C(=0)0-. In some embodiments, a photo-click tagged compound herein comprises a small molecule covalently linked to a photo-click tag by an ester. [0061] The term "ether," as used herein, refers to the group -0- In some embodiments, a photo-click tagged compound herein comprises a small molecule covalently linked to a photo-click tag by an ether. [0062] The term "immunomodulatory drug" or "IMID" refers to any compound (e.g. small molecule) that can be classified as an immunomodulatory drug. In general, an immunomodulatory drug is an anti-inflammatory or antineoplastic compound that can modulate an immune response. Most immunomodulatory drugs are structurally and functionally similar to thalidomide. Thalidomide can exist as two enantiomers, R-thalidomide and S-thalidomide. Each enantiomer may exhibit a different function or interact with a specific drug target (e.g., protein). Thus, immunomodulatory drugs are often small molecule derivatives of R-thalidomide or S-thalidomide. Exemplary, non-limiting immunomodulatory drugs are (R/Sj-lenalidomide, (R/S)-pomalidomide, and (R/S)-apremilast. In some embodiments, the immunomodulatory drug is thalidomide. In some embodiments, the immunomodulatory drug is lenalidomide. In some embodiments, the immunomodulatory drug is S-lenalidomide. In some embodiments, the immunomodulatory drug is R- ienalidomide. In some embodiments, the immunomodulatory drug is pomalidomide. In some embodiments, the immunomodulatoiy drug is S- pomalidomide. In some embodiments, the immunomodulatoiy drug is R- pomalidomide. In some embodiments, the immunomodulatory drug is apremilast. In some embodiments, the immunomodulatory drug is S- apremilast. In some embodiments, the immunomodulatory drug is R- apremilast. [0063] The term "linker," as used herein, refers to a chemical group or a molecule linking two molecules or moieties, e.g., a small molecule and a photo-click tag. A linker may be, for example, a bond, an amino acid sequence, a peptide, or a polymer of any length and composition. In some embodiments, the linker is an organic molecule, functional group, polymer, or chemical moiety. [0064] The term "photo-conjugation moiety," as used herein, refers to any moiety that forms a reactive intermediate upon irradiation with light (i.e., "photo-activation"). These moieties may be referred to as "photoreactive" moieties. Examples of photoreactive moieties are aryl azides, azido-methyl-coumarins, benzophenones, anthraquinones, diazo compounds, diazirines, and psoralen derivatives. For example, an aryl azide (e.g., phenyl azide, ortho- hydroxyphenyl azide, meto-hydroxyphenyl azide, tetrafluorophenyl azide, o t/zo-nitrophenyl azide, and eta-nitrophenyl azide) forms a reactive nitrene groups that can initiate addition reactions with double bonds, insertion into C-H and N-H bonds, or ring expansion in the presence of a nucleophile (e.g., a primary amine). In general, aryl azides are photoactived upon irradiation with UV light with a wavelength of about 250 nm to about 350 nm. Photo- conjugation moieties, their uses, and chemical reactions are discussed in Bioconjugate Techniques, 3rd Ed. (2013) by Hermanson; which is incorporated by reference herein. [ 06 ] The term "protease" refers to any enzyme capable of hydro!yzing a peptide bond. In general, a proteases catalyzes the hydrolysis of peptide bonds (i.e., digests the protein) through a unique mechanism based on the catalytic residue present in the active site of the protease. Exemplary, non-limiting proteases and their catalytic residues are serine proteases, which use a serine alcohol, cysteine proteases, which use a cysteine thiol, threonine proteases, which use a threonine secondary alcohol, aspartic proteases, which use an aspartate carboxylic acid, glutamic proteases, which use a glutamate carboxylie acid, metailoproteases, which use a metal (e.g., zinc), and asparagine peptide lyases, which use an asparagine to perform an elimination reaction and do not require water. In some embodiments, the protease is a serine protease. In some embodiments, the serine protease is trypsin. In some embodiments, the serine protease is chymotrypsin. In some embodiments, the protease is an aspartic protease. In some embodiments, the aspartic protease s pepsin. In some embodiments, one protease s used to digest a protein. In some embodiments, more than one protease is used to digest a protein. [00661 The terms "protein," "peptide," and "polypeptide" are used interchangeably herein and refer to a polymer of amino acid residues linked together by peptide (amide) bonds. The terms refer to a protein, peptide, or polypeptide of any size, structure, or function. Typically, a protein, peptide, or polypeptide will be at least three amino acids long. A protein, peptide, or polypeptide may refer to an individual protein or a collection of proteins. One or more of the amino acids in a protein, peptide, or polypeptide may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxy! group, a phosphate group, a famesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation, functionalization, or other modification, etc. A protein, peptide, or polypeptide may also be a single molecule or may be a multi -molecular complex. In some embodiments, a protein comprises a homodimer or a heterodimer. A protein, peptide, or polypeptide may be just a fragment of a naturally occurring protein or peptide. A protein, peptide, or polypeptide may be naturally occurring, recombinant, or synthetic, or any combination thereof. A protein may comprise different domains, for example, a nucleic acid binding domain (e.g., the gR A binding domain of Cas9 that directs the binding of the protein to a target site) and a nucleic acid cleavage domain. In some embodiments, a protein comprises a proteinaceous pari, e.g., an amino acid sequence constituting a nucleic acid binding domain, and an organic compound, e.g., a compound that can act as a nucleic acid cleavage agent. In some embodiments, a protein comprises a iigand binding domain. In some embodiments, a protein comprises an active site (e.g., site of biological or enzymatic activity). In some embodiments, a protein comprises an aliosteric site (e.g., site of a protein that can bind to a iigand that can be remote from an active site). In some embodiments, the protein is an enzyme. In some embodiments, the protein is a receptor. In some embodiments, the protein is a reporter protein (e.g., GFP). Any of the proteins provided herein may be produced by any method known in the art. For example, the proteins provided herein may be produced via recombinant protein expression and purification. Methods for recombinant protein expression and purification are well known, and include those described by Green and Sambrook, Molecular Cloning: A Laboratory Manual (4 ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)), the entire contents of which are incorporated herein by reference. In some embodiments, the protein is present in vitro. In some embodiments, the protein is present in vivo. In some embodiments, the protein is present in a cell. In some embodiments, the protein is present in a ceil lysate. In some embodiments, the protein is present in a whole proteome (i.e., the entire complement of proteins that is or can be expressed by a cell, tissue, or organism). [0067] As used herein, the term "salt" refers to any and all salts, and encompasses pharmaceutically acceptable salts [0068] The term "pharmaceutically acceptable salt" refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al describe pharmaceutically acceptable salts in detail in J . Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids, such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids, such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisuifate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2- naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium,

+ and (C -4 alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxvlate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate [0069] The term "sample" may be used to generally refer to an amount or portion of something {e.g., a protein). A sample may be a smaller quantity taken from a larger amount or entity; however, a complete specimen may also be referred to as a sample where appropriate. A sample is often intended to be similar to and representative of a larger amount of the entity of which it is a sample. In some embodiments a sample is a quantity of a substance that is or has been or is to be provided for assessment (e.g., testing, analysis, measurement) or use. The "sample" may be any biological sample including tissue samples (such as tissue sections and needle biopsies of a tissue); ceil samples (e.g., cytologicai smears (such as Pap or blood smears) or samples of cells obtained by microdissection); samples of whole organisms (such as samples of yeasts or bacteria); or cell fractions, fragments or organelles (such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise). Other examples of biological samples include blood, serum, urine, semen, fecal matter, cerebrospinal fluid, interstitial fluid, mucous, tears, sweat, pus, biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy), nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from a first biological sample. In some embodiments a sample comprises cells, tissue, or cellular material (e.g., material derived from cells, such as a cell lysate, or fraction thereof). A sample of a cell line comprises a limited number of cells of that cell line. In some embodiments, a sample may be obtained from an individual who has been diagnosed with or is suspected of having a disease. [0070] The term "small molecule," as used herein, is an organic molecule that is less than about 2 kiiodaltons (kDa) in mass. In some embodiments, the small molecule is less than about 1.5 kDa, or less than about 1 kDa. In some embodiments, the small molecule is less than about 800 daitons (Da), 600 Da, 500 Da, 400 Da, 300 Da, 200 Da, or 100 Da. Often, a small molecule has a mass of at least 50 Da In some embodiments, a small molecule is non- polymeric. In some embodiments, a small molecule is not an amino acid. In some embodiments, a small molecule is not a nucleotide. In some embodiments, a small molecule is not a saccharide. In some embodiments, a small molecule contains multiple carbon-carbon bonds and can comprise one or more heteroatoms and/ or one or more functional groups important for structural interaction with proteins (e.g., hydrogen bonding), e.g., an amine, carbonyi, hydroxyl, or carboxyl group, and in some embodiments at least two functional groups. In some embodiments, the small molecule is an SAID, or a derivative thereof. In some embodiments, the small molecule is an immunomodulatory drug, or a derivative thereof. In some embodiments, the small molecule is a chemotherapeutic agent, or a derivative thereof. [0071] The ter "steroid," as used herein, refers to any compound with a core structure comprising four fused rings, wherein three of the four rings are cyclohexane rings and one of the four rings s a cyclopentane ring. Steroids can be classified functionally, such as corticosteroids or sex steroids. In some embodiments, the corticosteroid is a glucocorticoid. In some embodiments, the corticosteroid is a mineralocorticoid. In some embodiments, the steroid is an androgen, an estrogen, or a progestogen. In some embodiments, the androgen is testosterone. In some embodiments, the estrogen is estradiol or beta-estradiol. In some embodiments, the progestogen is progesterone. Steroids can also be classified based on their chemical composition (i.e., the number of carbon atoms present in the steroid). Exemplar}' classifications are cholestanes (27 carbon atoms, e.g., cholesterol), cholanes (24 carbon atoms, e.g., cholic acid), pregnanes (21 carbon atoms, e.g., progesterone), androstanes (19 carbon atoms, e.g., testosterone), and estranges (18 carbon atoms, e.g., estradiol).

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

[0072] Small molecules are the most prominent class of agents that are used as therapeutics for the treatment of a variety of diseases and conditions, accounting for nearly 90% of the therapeutics available in the pharmaceutical market. Many agents (e.g., small molecules) elicit cell-type specific pharmacology that may increase therapeutic efficacy or yield off target toxicity. However, direct observation of the structures that underpin the global molecular associations between the proteome and even common therapeutics, such as the non-steroidal anti-inflammatory drugs (NSAIDs), remain little understood. Presented herein are photo-click tags, compounds, and methods useful for mapping the small molecule interactome of a small molecule of interest. These methods generally involve labeling of a target protein with a photo-click tag that is conjugated to the small molecule of interest, and may be refered to throughout the present disclosure as Small Molecule Interactome Mapping by Photo-Affinity Labeling (SIM-PAL), or Minimally-Interfering Photo-Affinity Labeling (MI-PAL) when the smallest exemplified photo-click chemical tags provided herein are employed. These photo-click tags, photo-conjugated compounds, and methods can be applied in vivo to identify binding sites or protein-protein interactions within the complex cellular environment. For example, SIM-PAL uses (I) photochemical conjugation of small molecules throughout the whole proteome and (2) enrichment of the conjugated peptides for (3) targeted mass spectrometry-based assignment. In addition, these photo-click tags, photo-conjugated compounds, and methods amenable to map global binding sites for virtually any agent of interest.

Photo-Click Tags

[0073] The development of small, multi-functional photo-click tags that are readily incorporated into a small molecule scaffold has accelerated target identification for non- covalent agents that interact with one or more proteins in the proteome. In general, the multi functional photo-click tags comprise two functional moieties: a photo-conjugation moiety that can covalently capture the protein target (e.g., an enzyme that binds to a small molecule of interest, a receptor, an antibody, etc.), and a biocompatible handle (e.g., a click chemistry handle) for functionalization with a reporter molecule or affinity tag (e.g., a biotinylated affinity tag). A biocompatible handle (e.g., a click chemistry handle) may be designed to study biological processes in their native environment (e.g., in living cells). The photo- conjugation moiety may comprise, for example, an aryl azide, benzophenone, or diazirine moiety, which can generate a short-lived, highly reactive intermediate (e.g., a nitrene, carbene, or diradical intermediate) that covalently attaches itself to a nearby biomoiecule (e.g., a protein, nucleic acid, lipid). The biocompatible handle may be a click chemistry handle, for example, an alkyne, an alkene (e.g., a strained alkene or an activated alkene), a cyano moiety (-C ≡ ), or additional suitable click chernistn,' handles known in the art. Taken together, the photo-conjugation moiety and the click chemistry handle provide a multi functional "photo-click tag". The photo-click tag may comprise the structure:

wherein

m and n are each independently integers between 1-10, inclusive.

[0074] In some embodiments, m is 0, I, or 2 . I some embodiments, is 0, 1, or 2 . In some embodiments, m and n taken together provide a photo-click tag fewer than 10 carbons in length (i.e., a Ci-io a ky ), not including the click chernistn,' handle. In some embodiments, m and n taken together provide a photo-click tag fewer than 0 carbons in length (i.e., a C alkyl), not including the click chemistry handle. In some embodiments, the photo-click tag comprises a Ci-io alkyl. The term "alkyl" refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms ("Ci-io alkyl"). Examples of

Ci-6 alkyl groups include methyl (Ci), ethyl (C2), propyl (C ) (e.g., n-propyl, isopropyl), butyl

(C4) (e.g., n-butyl, tert-butyl, sec-butyl, iso-butyl), pentyi (C5) (e.g., n-pentyl, 3-pentanyl, amyl, neopentyl, 3-methyl -2-butanyl, tertian,' amy!), and hexyl (C6) (e.g., n-hexyl).

Additional examples of alkyl groups include n-heptyl (C7), n-octyl (Cg), and the like. In some embodiments, the photo-click tag comprises a C3-7 alkyl, not including the click chemistry handle. In some embodiments, the photo-click tag comprises a C 3 alkyl, not including the click chemistry handle. In some embodiments, the photo-click tag comprises a C4 alkyl, not including the click chemistry handle. In some embodiments, the photo-click tag comprises a

C 5 alkyl, not including the click chemistry handle. In some embodiments, the photo-click tag comprises a C alkyl, not including the click chemistry handle. In some embodiments, the photo-click tag comprises a € 7 alkyl, not including the click chemistry handle. For example, in some embodiments, m is I and n is 1 to provide a photo-click tag that is 3 carbon atoms in length (C3 alkyl). Without wishing to be bound by any particular theory, photo-click tags with small scaffolds could provide the added benefit of reduced perturbation of small molecule binding to a protein target when the small molecule is bound to the photo-click tag. For example, integration of a small photo-click tag can preserve the native interaction between the small molecule conjugated to the photo-click tag and the target protein(s). See Examples 1 and 2 .

[0075] In some embodiments, X is -OH. In some embodiments, X is - 2. In some embodiments, X is halogen. In some embodiments, X is chlorine (CI). In some embodiments, X is iodine (I). In some embodiments, X is fluorine (F). In some embodiments, X is bromine (Br). [0076] Thus, in one aspect, provided herein are photo-click tags comprising (a) a photo- conjugation moiety, and (b) a click chemistry handle. In some embodiments, the photo- conjugation moiety is a diazirine moiety. In some embodiments, the photo-click tag comprises (a) a diazirine moiety, and (b) a click chemistry handle. In some embodiments, the click chemistry handle is an aikyne. In some embodiments, the photo-click tag comprises (a) a diazirine moiety, and (b) an aikyne. An "aikyne" is a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more carbon-carbon triple bonds (e.g., 1, 2, 3, or 4 triple bonds) ("C2-10 alkynyl"). In some embodiments, an aikyne group has 2 to 9 carbon atoms ("C2-9 aikyne"). In some embodiments, an aikyne has 2 to 8

-8 carbon atoms ("C 2 aikyne"). In some embodiments, an aikyne has 2 to 7 carbon atoms ("C 2- 7 alkynyl"). In some embodiments, an aikyne has 2 to 6 carbon atoms ("C2-6 aikyne"). In some embodiments, an aikyne has 2 to 5 carbon atoms ("C2-5 aikyne"). In some embodiments, an aikyne has 2 to 4 carbon atoms ("C2-4 aikyne"). In some embodiments, an aikyne has 2 to 3 carbon atoms ("C2-3 aikyne"). In some embodiments, an aikyne has 2 carbon atoms ("C 2 aikyne"). The one or more carbon-carbon triple bonds can be internal (such as in 2-butyne) or terminal (such as in 1-butyne). Examples of C2-4 aikynes include, ( ' without limitation, ethyne (C ), 1-propyne ( . 2-propyne (C3), 1-butyne (C4), 2-butyne (C ), and the like. Examples of ( ··..:, alkynes include the aforementioned C2-4 alkyne groups as well as pentyne (C5), hexyne (C6), and the like. Additional examples of alkynes include heptyne (C ), octyne (Cg), and the like. Unless otherwise specified, each instance of an alkyne is independently unsubstituted (an "u substituted alkyne") or substituted (a "substituted alkyne") with one or more substituents. In certain embodiments, the alkyne is an unsubstituted C2-J 0 alkyne. In certain embodiments, the alkyne is an unsubstituted C2 alkyne. In certain embodiments, the alkyne is a substituted C2-10 alkyne. [0077] In some embodiments, any of the photo-click tags provided herein may be optionally substituted with one or more electronegative atoms. In some embodiments, the photo-click tag s optionally substituted with one electronegative atom. In some embodiments, the photo- click tag is optionally substituted with two electronegative atoms. The electronegative atoms may be attached to the same carbon, or the electronegative atoms may be attached to two different carbons, as valency permits. In some embodiments, one or more of the electronegative atoms is fluorine. In some embodiments, the photo-click tag is optionally substituted with one fluorine atom. In some embodiments, the photo-click tag is optionally substituted with two fluorine atoms. The fluorine atoms may be attached to the same carbon, or the fluorine atoms may be attached to two different carbons, as valency permits. Placing the one or more fluorine atoms in proximity to the diazirine moiety on the photo-click tag may improve photo-conjugation and/or click chemistry reaction kinetics, as photochemical carbene intermediates and click chemistry reaction kinetics are dependent on electronic substituent effects. See, e.g., Brunner J. etal. ( 9 ) J Biol Chem, 255, pp. 33 13-3318. Without wishing to be bound by any particular theoiy, electronically tuning the photo-click tag by placing one or more fluorine substituents on the carbon atom adjacent to the diazirine moiety could provide a more reactive photo-click tag, thereby increasing its utility as a photo- click tag, particularly in in vivo applications or applications in whole proteomes where there are a large number of proteins and other biomolecules present {e.g., in a cell, tissue, or organism). In some embodiments, the photo-click tag is of the formula: [0078] In some embodiments, the photo-conjugation moiety (M) is an aryl azide, azido- methyl-coumarin, benzophenone, anthraquinone, diazo compound, diazirine, or psoralen derivative. In some embodiments, the photo-conjugation moeity (M) is a diazirine moeity. [0079] Diazirines are a c ass of organic sma molecules comprising a carbon bound to two nitrogen atoms, wherein the two nitrogen atoms are double bonded to one another, thus forming a three-membered heterocyclic ring. In some embodiments, the diazirine moiety

comprises the staicture: . Upon irradiation with a specific wavelength of light (e.g., ultraviolet light), a diazirine forms a reactive carbene species (see Scheme I below). In some embodiments, the reactive carbene species comprises the upon irradiation with a specific wavelength of light. In some embodiments, the reactive carbene species comprises at least two free electrons. In some embodiments, the specific wavelength of light is between about 10 rati and about 400 m . In some embodiments, the specific wavelength of light is between about 355 nm and about 365 nm. In some embodiments, the specific wavelength of light is about 355 nm. In some embodiments, the specific wavelength of light is about 365 nm.

[0080] In some embodiments, the reactive carbene species reacts with a C-C, C-H, N-H, or O-H bond of a protein. Upon insertion of the reactive carbine species into a C-C, C-H, N-H, or O-H bond of a protein, a new covalent bond between the protein and photo-click tag is formed, thereby linking the photo-click tag to the protein (see, e.g., Figure 30). This process may be referred to as photoaffinity labeling (PAL) (Dubinsky et al. (201 ) Diazirine based photoaffmity labeling. BioorgMed Chem, 20 pp. 554-570). A non-limiting example of a photo-conjugation of a photo-click tag, or a compound conjugated to a photo-click tag, to a target protein is shown below in Scheme II. The reaction in Scheme II can be performed in vitro or in vivo.

[S represents a small molecule conjugated to a group comprising a diazirine moiety (e.g., a photo-click tag), R represents an oxygen, nitrogen, or carbon atom in amino acid in the target protein]

0081] In some embodiments, the photo-click tag is of the formula:

wherein,

X is -GH, -NH 2, or a halogen.

[0082] In some embodiments, X is -OH. In some embodiments, X is - H2. n some embodiments, X is halogen. In some embodiments, X is chlorine (CI). In some embodiments, X is iodine (I). In some embodiments, X is fluorine (F). I some embodiments, X is bromine (Br). A person of skill in the art will recognize the appropriate X group for use in a photo- click tag in accordance with the present disclosure based on the functional groups present in the agent to be conjugated to the photo-click tag. For example, Figure 26 shows exemplary synthetic schemes that can be used to conjugate a photo-click tag wherein X is -NH 2 to a small molecule comprising an -OH group, thereby generating a photo-conjugated agent compri ssiinngg a -O- linker between the small molecule and the photo-click ta;

s83 j In some embodiments, w/herein X is I , the photo-click tag is of the formula:

In some embodiments, herein X is -NH 2, the hoto-click ta is of the formula:

085] I n some embodiments, the photo-cl ick tag is o f the formula:

[ In some embodiments, the photo-click tag is of the formula: n some embodiments, the photo-click tag optionally comprises one or more electronegative atoms (e.g., fluorine).

[0087] In some embodiments, the photo-click tag is of the formula: In some embodiments, the photo-click tag optionally comprises one or more electronegative atoms (e.g., fluorine).

[0088] In some embodiments, the photo-click tag is of the formula: . In some embodiments, the photo-click tag optionally comprises one o r more electronegative atoms (e.g., fluorine). N~N OH [0089] In some embodiments, the photo-click tag is of the formula: . In some embodiments, the photo-click tag optionally comprises one or more electronegative atoms

(e.g., fluorine).

N= N

[0090] In some embodiments, the photo-click tag is o f the formula: 2 . some embodiments, the photo-click tag optionally comprises one or more electronegative atoms (e.g., fluorine). [0091] In some embodiments, the photo-click tag is of the formula: some embodiments, the photo-click tag optionally comprises one or more electronegative atoms (e.g., fluorine).

N= N

[0092] In some embodim ents, the photo-click tag is of the formula: . n some embodiments, the photo-click tag optionally comprises one or more electronegative atoms (e.g., fluorine).

H2 0093] In some embodim ents, the photo-click tag is of the formula: . In some embodiments, the photo-click tag optionally comprises one or more electronegative atoms

(e.g., fluorine). N-N

94] In some embodiments, the photo-click tag is of the formula: . In some embodiments, the photo-click tag optionally comprises one or more electronegative atoms (e.g., fluorine).

|0095| In some embodiments, the photo-click tag is of the formula: [0096] In some embodiments, for example, when the photo-click tag is associated with a small molecule of interest, the photo-click tag is coupled to the small molecule through a linker, as described below. Thus, in some embodiments, the photo-click tag is of the formula:

[0097] In some embodiments, the photo-click tag is less than about 10 A in le gth in some embodiments, the photo-click tag is less than about 9.5 A in length. In some embodiments, the photo-click tag is less than about 9 A in length. In some embodiments, the photo-click tag is less than about 8 A in length. In some embodiments, the photo-click tag is less than about 7 A in length. In some embodiments, the photo-click tag is less than about 6 A in length. In some embodiments, the photo-click tag is between about 6 A and about 9.5 A in length. In some embodiments, the photo-click tag is between about 6 A and about 8 A in length. In some embodiments, the photo-click tag is between about 6 A and about 7 A in length. In some embodiments, the photo-click tag is about 7 A in length. In some embodiments, the photo-click tag is about 6.9 A in length.

Compounds Comprising Photo-Click Tags [0098] As discussed above, the photo-click tags presented herein comprise a photo- conjugation moiety that can covalently capture (i.e., bind) the protein target (e.g., an enzyme that binds to a small molecule of interest, a receptor, an antibody, etc.), and a biocompatible handle (e.g., a click chemistry handle) for functionalization with a reporter molecule or affinity tag (e.g., a biotinylated affinity tag). Without wishing to be bound by any particular theory, the affinity can be used to enrich the target protein of interest, and aid in identifying the target protein bound to the photo-click tagged agent of interest. When attached to a compound (e.g., small molecule) of interest, these "photo-click tagged compounds" can be used to map the interactions of the compound of interest with the target molecule (e.g., a protein). These photo-click tagged compounds are useful, for example, for mapping the interactions of the compound in a whole proteome, or for mapping the proteomic interactions mediated by the compound in vivo. Some compounds (e.g., small molecule drugs) can exist as stereoisomers (e.g., epimers, diastereomers, or enantiomers), wherein each stereoisomer may exhibit a different activity (e.g., bind to different target protein). In some embodiments, a compound exists as an enantiomer, wherein the S- and R-enantiomer interact differently with the same target protein. In some embodiments, a compound exists as an enantiomer, wherein the S- and R-enantiomer interact with unique target proteins. Thus, the compounds and methods of the present invention can be useful in determining the action of a specific enantiomer or other stereoisomer of a small molecule (e.g., an immunomodulatory drug). For example, the orientation of each enantiomer may place the photo-conjugation (e.g., diazirine) moiety in close proximity to one or more specific amino acids of the target protein (e.g., in the active site, in an allosteric site). A difference in the amino acids bound by the photo- conjugation moiety could indicate enantiomer-specific binding and interactions with the target protein. [0099] Mos small molecules can be covalently coupled to a photo-click tag provided herein by employing the appropriate organic chemistry reaction to couple the small molecule to the photo-click tag, for example, as shown in Figures 26, 70, and 71. Conjugation of the photo- click tag to the small molecule can be achieved by formation of an ester, ether, amine or amide to link the small molecule to the photo-click tag. For example, as shown in Figure 26, an ether bond is formed when a photo-click probe comprising a free amine (NH2) group reacts with a free hydroxyl (OH) group on the small molecule. As another example, an amide bond is formed when a photo-click probe comprising a free amine ( H2) group reacts with a free carboxylic acid (-COOH) group on the small molecule (Figure 26). A person of ordinary skill in the art will be able to determine the appropriate reaction conditions to use for coupling a small molecule to a photo-click tag (e.g., a triisopropyl ether (TIPS) protected photo-click tag) based on the functional groups present in the small molecule of interest, or portion of the small molecule that binds to a target protein or proteins. The photo-click tag should be placed on the molecule so as to not interfere with the small molecule-protein binding interaction. Thus, the resulting photo-click tagged compound may comprise the entire small molecule, or a portion of the small molecule. Where the photo-tagged compound comprises only a portion of the small molecule, this portion of the small molecule should be sufficient for maintaining the interaction between the small molecule and the target protein(s). [0100] Thus, in some aspects, provided herein are compounds comprising the structure of Formula (I):

wherein S is a small molecule, or derivative thereof; P is a photo-click tag comprising (a) a photo-conjugation moiety (M), and (b) a click chemistry handle; and L s a linker. [0101] In some embodiments, the click chemistry handle is an alkyne. Thus, in some

[0102] In some embodiments, the photo-conjugation moiety (M) is an aryl azide, azido- methyl-coumarin, benzophenone, anthraquinone, diazo compound, diazirine, or psoralen derivative. In some embodiments, the photo-conjugation moiety (M) is a diazirine moiety. In some embodiments, P comprises (a) a diazirine moiety, and (b) a click chemistry handle. In some embodiments, the click chemistry handle is an alkyne. In some embodiments, P comprises (a) a diazirine moiety, and (b) an alkyne.

.04] some embodiment,, P i. ' . to some e„*odi e„t , P optically comprises one or more electronegative atoms (e.g., fluorine)

N= N [0105] In some embodiments, P is . In some embodiments, P optionally comprises one or more electronegative atoms (e.g., fluorine).

)6j In some embodiments, P is . In some embodiments, P optionally comprises one or more electronegative atoms (e.g., fluorine).

[0107] In some embodiments, P is

'8] In some embodiments, L is a bond. In some embodiments, L comprises an ester, an ether, an amine, or an amide. In some embodiments, L comprises an ester. In some embodiments, L comprises an ether. In some embodiments, L comprises an amine. In some

embodiments, L comprises an amide. In some embodiments, L is

. In some embodiments, L is . In some embodiments, L is . In some

embodiments, L is [0109] In some embodiments, S is an antibiotic, an anti-proliferative agent, an anti-cancer agent, a chemotherapeutic agent, an anti-angiogenesis agent, an anti -inflammatory agent, an immunosuppressant, an immunomodulatory agent, an anti-bacterial agent, an anti-viral agent, a cardiovascular agent, a cholesterol-lowering agent, an anti-diabetic agent, an anti-allergic agent, a contraceptive agent, or a pain-relieving agent. [0110] In some embodiments, S is an anti-inflammatory agent, or derivative thereof. In some embodiments, the anti-inflammatory agent is a non-steroidal anti-inflammatory drug (NSAID) , or derivative thereof. Exemplary, non-limiting examples of NSAIDs for use herein are aspirin (acetylsalicylic acid), diflunisal (dolobid), salicylic acid and other salicylates, sal sal ate (disalcid), ibuprofen, dexibuprofen, naproxen, fenoprofen, ketoprofen, dexketoprofen, flurbiprofen, oxaprozin, loxoprofen, indomethacin, tolmetin, sulindac, etodolac, ketorolac, diclofenac, aceclofenac, nabumetone, piroxicam, meloxicam, tenoxicam, droxicam, lornoxicam, isoxicam, phenylbutazone (bute), mefenamic acid, meclofenamic acid, flufenamic acid, tolfenamic acid, celecoxib, rofecoxib, vaidecoxib, parecoxib, lumiracoxib, etoricoxib, firocoxib, nimesulide, clonixin, licofelone, and derivatives thereof. In some embodiments, the NSAID is selected from the group consisting of acetaminophen, aspirin, bromefenac sodium, celecoxib, diclofenac, diclofenac potassium, diclofenac sodium, diflunisal, etodolac, fenoprofen calcium, flurbiprofen, ibuprofen, indomethacin, ketoprofen, magnesium salicylate, meclofenamate sodium, mefenamic acid, nabumetone, naproxen, naproxen sodium, oxaproxin, oxyohebutazone, phenylbutazone, piroxicam, rofecoxib, salsalate, sodium salicylate, sulindac, tometin sodium, vaidexocib, and derivatives thereof. [0111] In some embodiments, the NSAID is naproxen, or derivative thereof. In some embodiments, the NSAID is celecoxib, or derivative thereof. In some embodiments, the NSAID is indomethacin, or derivative thereof. [0112] In some embodiments, the compound is of the formula: or a pharmaceutically acceptable salt thereof. [0113] In some embodiments, the anti-inflammatory agent is a steroidal anti-inflammatory agent, or derivative thereof. In some embodiments, the steroidal anti -inflammatory agent is a corticosteroid, or derivative thereof. Exemplary, non-limiting corticosteroids suitable for use herein are 21- acetoxypregnenolone, alclometasone, alclometasone dipropionate, algestone, amcinonide, beclomethasone, betamethasone, betamethasone dipropionate, betamethasone sodium phosphate, betamethasone valerate, budesonide, chloroprednisone, ciclesonide, clobetasoi, clobetasol-17- propionate, clobetasone-17-butyrate, clobetasone, clocortolone, cloprednol, corticosterone, cortisone, cortisone acetate, cortivazol, deflazacort, desonide, desoximetasone, dexamethasone, dexamethasone sodium phosphate, diflorasone, diflucortolone, difluprednate, enoxolone, fluazacort, flucloronide, flumethasone, fluoeinonide, fluocinolone, fluocinolone acetonide, fluocinonide, fluocortin butyl, fluocortolone, fluocortolone caproate, fluocortolone pivalate, fluorornetholone, flunisolide, fluperolone acetate, fluprednidene acetate, fluprednisolone, flurandrenolide, fluticasone propionate, formocortai, halcinonide, haiobetasol propionate, halometasone, halopredone acetate, hydrocortamate, hydrocortisone, hydrocortisone acetate, hydrocortisone- 17- aceponate, hydrocortisone- 17-buteprate, hydrocortisone- 17-butyrate, hydrocortisone- 17- valerate, loteprednol, mazipredone, medrysone, meprednisone, methylprednisolone, mometasone, mometasone furoate, paramethasone, paramethasone acetate, prednicarbate, prednisolone, prednisolone 25-diethylamino-acetate, prednisolone sodium phosphate, prednisone, prednival, prednylidene, rimexolone, tixocortol, tixocortol pivalate, triamcinolone, triamcinolone acetomde, triamcinolone alcohol, triamcinolone benetonide, triamcinolone hexacetonide, and derivatives thereof. [0114] In some embodiments, S is an immunomodulatory drug, or derivative thereof. In some embodiments, the immunomodulatory drug is thalidomide, lenalidomide, pomalidomide, or derivative thereof. In some embodiments, the lenalidomide is R- lenalidomide. In some embodiments, the lenalidomide is S-lenalidomide. In some embodiments, the lenalidomide is R-pomalidomide. In some embodiments, the lenalidomide is S-pomalidomide. j j In some embodiments, the compound is of the formula: or a pharmaceutically acceptable salt thereof, wherein represents a bond of un specified stereochemistry. [0116] n some embodiments, the compound is of the formula: O O O or a pharmaceutically acceptable salt thereof. [0117] In some embodiments, S is a chemotherapeutic agent, or derivative thereof. Exemplar}- chemotherapeutic agents include, but are not limited to, anti -estrogens (e.g. tamoxifen, raloxifene, and megestrol), LHRH agonists (e.g. goscrclin and leuprolide), anti- androgens (e.g. flutamide and bicalutamide), photodynamic therapies (e.g. vertoporfin (BPD- MA), phthalocyanine, photosensitizer Pc4, and demethoxy-hypocrellin A (2BA-2-DMHA)), nitrogen mustards (e.g. cyclophosphamide, ifosfamide, trofosfamide, chlorambucil, estramustine, and melphalan), nitrosoureas (e.g. carmustine (BCNU) and lomustine (CCNU)), alkylsulphonates (e.g. busulfan and treosulfan), triazenes (e.g. dacarbazine, temozolomide), platinum containing compounds (e.g. cisplatin, carboplatin, oxaliplatin), vinca alkaloids (e.g. vincristine, vinblastine, vindesine, and vinorelbine), taxoids (e.g. paclitaxei or a paciitaxei equivalent such as nanoparticie albumin-bound paclitaxel (ABRAXANE), docosahexaenoic acid bound-paciitaxei (DHA-paclitaxel, Taxoprexin), polyglutamate bound-paclitaxel (PG-paclitaxel, paciitaxei poiigiumex, CT-2103, XYOTAX), the tumor-activated prodrug (TAP) ANG1005 (Angiopep-2 bound to three molecules of paciitaxei), paciitaxei -EC- 1 (paciitaxei bound to the erbB2-recognizing peptide EC-1 ), and glucose-conjugated paclitaxel, e.g., 2'-paclitaxei methyl 2-glucopyranosyl succinate; docetaxel, taxol), epipodophyllins (e.g. etoposide, etoposide phosphate, teniposide, topotecan, 9-aminocamptothecin, camptoirinotecan, innotecan, crisnatol, mitomycin), anti-metabolites,

DHFR inhibitors (e.g. methotrexate, dichloromethotrexate, trimetrexate, edatrexate), IMP dehydrogenase inhibitors (e.g. mycophenolic acid, tiazofurin, ribavirin, and EICAR), ribonuclotide reductase inhibitors (e.g. hydroxyurea and deferoxamine), uracil analogs (e.g. 5-iluorouracil (5-FU), fioxuridine, doxifluridine, ratitrexed, tegafur-uracil, capecitabine), cytosine analogs (e.g. cytarabine (ara C), cytosine arabinoside, and fludarabine), purine analogs (e.g. mercaptopurine and Thioguanine), Vitamin D3 analogs (e.g. EB 1089, CB

1093, and K 1060), isoprenylation inhibitors (e.g. iovastatin), dopaminergic neurotoxins

(e.g. 1-methyI-4-phenyipyridinium ion), cell cycle inhibitors (e.g. staurosporine), actinomycin (e.g. actinomycin D, dactinomycin), bleomycin (e.g. bleomycin A2, bleomycin

B2, peplomycin), anthracycline (e.g. daunorubicin, doxorubicin, pegylated liposomal doxorubicin, idarubicin, epirubicin, pirarubicin, zorubicin, mitoxantrone), MDR inhibitors

(e.g. verapamil), Ca2+ ATPase inhibitors (e.g. thapsigargin), imatinib, thalidomide, lenalidomide, tyrosine kinase inhibitors (e.g., axitinib (AG013736), bosutinib (SKI-606), cediranib (RECENTIN™, AZD2I71), dasatinib (SPRYCEL®, BMS-354825), erlotinib (TARCEVA®), gefitinib (IRESSA®), imatinib (Gleevec®, CGP57148B, STI-571), lapatinib

(TYKERB®, TYVERB®), lestaurtinib (CEP-701), neratinib ( 1 - 72 , nilotmib (TASIGNA®), semaxanib (semaxinib, SU5416), sunitinib (SUTENT®, SU1 1248), toceramb (PALLADIA®), vandetanib (ZACTIMA®, ZD6474), vatalanib (PTK787, PTK/ZK), trastuzumab (HERCEPTIN®), bevacizumab (AVASTIN®), rituximab (RITUXAN®), cetuximab (ERBITUX®), panitumumab (VECTIBIX®), ranibizumab (Lucentis®), nilotinib (TASIGNA®), sorafenib (NEXAVAR®), everoiimus (AFINITOR®), alemtuzumab (CAMPATH®), gemtuzumab ozogamicin (MYLOTARG®), temsirolimus (TORISEL®), ENMD-2076, PCI-32765, AC220, dovitinib lactate (TKI258, CFflR-258), BIBW 2992 (TOVOK™), SGX523, PF-04217903, PF-02341066, PF-299804, BMS-777607, ABT-869, MP470, BIBF 20 ( ARGATEF ®), AP24534, JNJ-26483327, MGCD265, DCC-2036, BMS-690154, CEP-1 1981, tivozamb (AV-951), OSI-930, MM-121, XL-I84, XL-647, and/or

XI. 28), proteasome inhibitors (e.g., bortezomib (VELCADE)), mTOR inhibitors (e.g., rapamycin, temsirolimus (CCI-779), everoiimus (RAD-001), ridaforolimus, AP23573 (An ad), AZD8055 (AstraZeneca), BEZ235 (Novartis), BGT226 (Norvartis), XL765 (Sanofi Aventis), PF-4691502 (Pfizer), GDC0980 (Genetech), SF1 126 (Semafoe) and OSI-027 (OSI)), oblimersen, gemcitabine, carminomycin, leucovorin, pemetrexed, cyclophosphamide, dacarbazine, procarbizine, prednisolone, dexamethasone, campathecin, plicamycin, asparaginase, aminopterin, methopterin, porfiromycin, melphalan, leurosidine, leurosine, chlorambucil, trabectedin, procarbazine, discodermolide, carminomycin, aminopterin, hexamethyl melamine, and derivatives thereof. [0118] In some embodiments, the chemotherapeutic agent is daunorubicin, or derivative thereof In some embodiments, the chemotherapeutic agent is mitomycin, or derivative thereof [0119] In some embodiments, the compound is of the formula: or a pharmaceutically acceptable salt thereof [0120] In some embodiments, S is a steroid. In some embodiments, the steroid is a sex steroid, or derivative thereof. In some embodiments, the sex steroid is an estrogen, or derivative thereof. In some embodiments, the estrogen is estradiol or beta-estradiol, or derivative thereof. [0121] In some embodiments, the compound is of the formula:

or a pharmaceutically acceptable salt thereof. [0122] Any of the compounds presented herein can comprise one or more isotopically labeled atoms. In some embodiments, the isotopically labeled atom is N, 1 C, 1 F, or H . For example, as shown in Figure 6A, nitrogen atoms labeled with astericks (*) indicate N nitrogen atoms. Isotopic labeling of o e or more atoms in the compound can faci litate identification of the compound through biophysical methods that are senstivie to isotopes, such as NMR. For example, NMR can be used to confirm the identity and structure of the appropriate photo-click tag or photo-click tagged compound product generated by the synthesis reaction (see, e.g., Examples 1 and 2). In addition, isotope-targeted mass spectrometry (MS) can be used to identify and assign the constitutive peptides of the target protein that are conjugated to the photo-click tagged compound {Example 1). [0123] In another aspect, provided herein are amino acid analogs comprising the structure of Formula (Il-a): wherein P is a photo-click tag comprising (a) a photo-conjugation moiety (M), and (b) a click chemistry handle [0124] In another aspect, provided herein are amino acid analogs comprising the structure of Formula (II-b):

wherein P is a photo-click tag comprising (a) a photo-conjugation moiety (M), and (b) a click chemistry handle.

[0125] In general, L-amino acids are incorporated into proteins in mammalian (e.g., human) ceils. While L-amino acids represent ail of the amino acids found in proteins during translation in the ribosome, D-amino acids are found in some proteins produced by enzyme posttransiationai modifications after translation and translocation to the endoplasmic reticulum. Thus, in some embodiments, the amino acid analog comprises the structure of Formula (II-a). Alternatively, in some embodiments, the amino acid analog comprises the structure of Formula (II-b). [0126] In some embodiments, the click chemistry handle is an alkyne. Thus, in some

[0127] In some embodiments, the photo-conjugation moiety (M) is an_aryl azide, azido- methyl-coumarin, benzophenone, anthraquinone, diazo compound, diazirine, or psoralen derivative. In some embodiments, the photo-conjugation moiety (M) is a diazirine moiety. In some embodiments, P comprises (a) a diazirine moiety, and (b) a click chemistry handle. In some embodiments, the click chemistry handle is an alkyne. In some embodiments, P comprises (a) a diazirine moiety, and (b) an alkyne.

[0128] In some embodiments, P is

In some embodiments, P is In some embodiments, P optionally comprises one or more electronegative atoms (e.g., fluorine).

|0130| In some embodiments, P is optionally comprises one or more electronegative atoms (e.g., fluorine).

31] In some embodiments P is In some embodiments, P optionally comprises one or more electronegative atoms (e.g., fluorine).

[0132] In some embodiments, is [0133] In some embodiments, the amino acid analog is of the formula:

[0134] Also encompassed by the disclosure are kits. The kits provided may comprise a photo-click tag, a compound of Formula (I), or an amino acid analog of Formula -a) or (II- b), described herein; and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, the kit comprises a photo-click tag provided herein. In some embodiments, the kit comprises a compound of Formula (I) provided herein. In some embodiments, the kit comprises an amino acid analog of Formula (Il-a) provided herein. In some embodiments, the kit comprises an amino acid analog of Formula (Il-b) provided herein. In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of a photo-click tag or photo-tagged compound described herein. In certain embodiments, a kit described herein further includes instructions for using the kit. In certain embodiments, the kits and instructions provide for carrying out a method described herein.

Methods for determining small molecule-protein and. protein-protein interactions [0135] As described above the photo-click tags and photo-click tagged compounds described herein are useful for mapping the direct and indirect effects of small molecules within the proteome. Some aspects of the present disclosure provide a small photo-click tag, wherein the photo-click tag is linked to a small molecule, that enables efficient capture, enrichment, and characterization of small molecule binding sites on a target protein or proteins. These methods can also be applied to determine the target protein of a small molecule, wherein the mechanism of action and/or the protein targeted by the small molecule is not known or well characterized. In addition, the methods and compositions provided herein are useful in determining a protein-protein interaction map, for example, i the presence of a small molecule to determine how the small molecule impacts cellular signaling and/or protein- protein interactions within a cell. [0136] In one aspect, provided herein is a method for identifying the target protein of a small molecule. In some embodiments, the method comprises: (i) providing a compound comprising the small molecule connected to a photo-click tag via a linker, wherein the photo- click tag comprises (a) a photo-conjugation moiety and (b) a click chemistry handle, (ii) activating the photo-conjugation moiety by irradiating the compound of (i) with a specific wavelength of light; (iii) contacting the target protein with the activated compound of (ii); (iv) forming a complex through a photo-induced covalent bond between the activated compound of (ii) and the protein; and (v) identifying the complex produced in (iv) that is bound to the compound, thereby identifying the target protein of the small molecule. In some embodiments, the photo-conjugation moiety is a diazirine moiety. In some embodiments, the photo-click tag comprises (a) a diazirine moiety and (b) a click chemistry handle. In some embodiments, the click chemistry handle is an alkyne. In some embodiments, the photo-click tag comprises (a) a diazirine moiety and (b) an alkyne. [0137] In another aspect, provided herein is a method for identifying the binding site of a small molecule to a protein. In some embodiments, the method comprises: (i) providing a compound comprising the small molecule connected to a photo-click tag via a linker, wherein the photo-click tag comprises (a) a photo-conjugation moiety, and (b) a click chemistry handle, (ii) activating the photo-conjugation moiety by irradiating the compound of (i) with a specific wavelength of light; (iii) contacting the protein with the activated compound of (ii); (iv) forming a complex through a photo-induced covalent bond between the activated compound of (ii) and the protein; (v) digesting the protein of the complex into constitutive peptides in the presence of a protease; and (vi) identifying the one or more peptides produced in (v) that are bound to the compound of (i), thereby identifying the protein binding site of the small molecule. In some embodiments, the photo-conjugation moiety is a diazirine moiety. In some embodiments, the photo-click tag comprises (a) a diazirine moiety, and (b) a click chemistry handle. In some embodiments, the click chemistry handle is an alkyne. In some embodiments, the photo-click tag comprises (a) a diazirine moiety, and (b) an alkyne. [0138] In yet another aspect, provided herein is a method for identifying an interaction between a first protein and a second protein in a cell. In some embodiments, the method comprises: (i) providing a cel with an amino acid analog, wherein the amino acid analog comprises a photo-click probe comprising (a) a photo-conjugation moiety and (b) a click chemistry handle, and wherein the amino acid analog is incorporated into the first protein and/or the second protein during protein synthesis; (ii) activating the photo-conjugation moiety of the amino acid analog by irradiating the cell with a specific wavelength of light; (iii) contacting the first protein or the second protein with the activated compound of (ii); (iv) forming a protein-protein complex through a photo-induced covalent bond between the activated amino acid analog of the fi rst protein and a amino acid in the second protein; and (v) identifying the complex produced in (ii) that comprises the amino acid analog covalently linking the first protein and the second protein, thereby identifying the first protein and the second protein involved in the interaction. In some embodiments, the photo-conjugation moiety is a diazirine moiety. In some embodiments, the photo-click tag comprises (a) a diazirine moiety and (b) a click chemistry handle. In some embodiments, the click chemistry handle is an alkyne. In some embodiments, the photo-click tag comprises (a) a diazirine moiety and (b) an alkyne. In some embodiments, the method further comprises digesting the protein-protein complex into constitutive peptides in the presence of a protease; and identifying a conjugated peptide that comprises a peptide comprising the amino acid analog covalently linking a peptide of the first protein to a peptide of the second protein. In some embodiments, the method further comprises contacting the ceil with a small molecule, wherein the cell is contacted with the small molecule before the activating of step (ii). In some embodiments, the first protein and the second protein identified in the presence of the small molecule are compared to the first protein and the second protein identified in the absence of the small molecule. In some embodiments, a difference in the first protein and the second protein in the presence of the small molecule compared to the first protein and the second protein in the absence of the small molecule indicates modulation of a protein-protein interaction in the cell in the presence of a small molecule. In some embodiments, the first protein or the second protein is enriched in the presence of a small molecule. In some embodiments, the enrichment is at least 2-fold, at least 3-fold, at least 4-fold, or at least 5-fold compared to the amount of the first protein or the second protein in the absence of the small molecule. In some embodiments, the small molecule is an antibiotic, an anti-proliferative agent, an anti -cancer agent, a chemotherapeutic agent, an anti-angiogenesis agent, an anti¬ inflammatory agent, an immunosuppressant, an immunomodulatory agent, an anti-bacterial agent, an anti-viral agent, a cardiovascular agent, a cholesterol-lowering agent, an anti diabetic agent, an anti-allergic agent, a contraceptive agent, or a pain-relieving agent. In some embodiments, the small molecule is an anti-inflammatory agent, an immunomodulatory drug, a chemotherapeutic agent, or a derivative thereof. In some embodiments, the small molecule is an anti-inflammatory agent, or derivative thereof. In some embodiments, the small molecule is an immunomodulatory drug, or derivative thereof. In some embodiments, the small molecule is a chemotherapeutic agent, or derivative thereof. In some embodiments, the small molecule is a steroid, or derivative thereof. [0139] In some embodiments, the diazirine moiety forms a reactive carbene species upon irradiation with a specific wavelength of light. In some embodiments, the reactive carbene species reacts with a C-C, C-H, N-H, or bond of a protein. Upon insertion of the reactive carbene species into a C-C, C-H, N-H, or O-H bond of a protein, a new photo- induced covalent bond between the protein and photo-click tag is formed, thereby linking the compound comprising the photo-click tag to the protein to generate a complex. In some embodiments, the specific wavelength of light is between about 10 nm and about 400 nm. In some embodiments, the specific wavelength of light is between about 355 nm and about 365 nm. In some embodiments, the specific wavelength of light is about 355 nm. In some embodiments, the specific wavelength of light is about 365 nm. [0140] In some embodiments, the photo-click tag of (i) s of the formula:

irradiation with light. In N~N some embodiments, the diaziiine moiety *· forms the reactive carbene species

upon irradiation with light. In some embodiments, the photo-click tag of (ii comprising the activated diazirine moiety is of the formula:

or after irradiation with light. In

some embodiments, the photo-click tag of (i) is of the formui before irradiation with light, and is of the formula after irradiation with light. In

N= N some embodiments, the photo-click tag of (i) is of the formula before irradiation with light, and is of the formula after irradiation with light. In some N-N embodiments, the photo-click tag of (i) is of the formula before irradiation with ight, and is of the formula *- after irradiation with light. In some embodiments, the photo-click tag of (i) is of the formula before irradiation with light, and is of

the formula after irradiation with light. In some embodiments, the photo-click

tag of (i) is of the formula before irradiation with iight, and is of the formula

after irradiation with light. In some embodiments, the photo-click tag of (i) is of

before irradiation with light, and is of the formula

after irradiation with light. In some embodiments, the photo-click tag of

of the formula irradiation with iight and is of the formula

after irradiation with light. In some embodiments, the photo-click tag of

(i) is of the formula before irradiation with light, and is of the formula

after irradiation with light. In some embodiments, the photo-click tag of (i) is

of the formula efore irradiation with light, and is of the formula after irradiation with light. In some embodiments, the photo-click tag of (i) s of the formula

before irradiation with iight, and is of the formula after irradiation with light. In some embodiments, the photo-click tag of (i) is of the formula

before irradiation with iight, and is of the formula after irradiation with light. In some embodiments, the photo-click tag of (i) is of the formula

before irradiation with light, and is of the formula adiation with light. In some embodiments, the photo-click tag of (i) is of the formula

before irradiation with light, and is of the formula after irradiation with light. In some embodiments, the light has a wavelength between about 0 n and about 400 nm. In some embodiments, the light has a wavelength between about 355 nm and about 365 nm. In some embodiments, the light has a wavelength of about 355 nm. In some embodiments, the light has a wavelength of about 365 nm. [0141] Some embodiments of the method comprise contacting the protein conjugated to the compound comprising the small molecule and photo-click tag or the protein-protein complex formed in the presence of an amino acid analog with a protease to digest the proteins into constitutive peptides. Without washing to be bound to any particular theory, protease digestion is a step often employed before analysis and identification of the protein using mass spectrometry (MS). Digestion of the protein into constitutive peptides allows for MS analysis of individual peptides, which can allow for the identification of peptides bound to photo-click tag and thus the small molecule or protein partner (i.e., protein-protein interaction partner) of interest. This method is also used, for example, to identify protein post-translational modifications. See, e.g., Gundry RL, etal. (2009) Preparation of Proteins and Peptides for Mass Spectrometry Analysis in a Bottom-Up Proteomics Workflow. C rr Protoc Mol Biol, doi: 10.1002/0471 142727.mbl025s88; which is incorporated by reference herein. In some embodiments, the protease is a serine protease, cysteine protease, threonine protease, aspartic protease, glutamic protease, metalloprotease, or an asparagine peptide lyase. In some embodiments, the protease is a serine protease. In some embodiments, the serine protease is trypsin. In some embodiments, the serine protease is chymotrypsin. some embodiments, the protease is an aspartic protease. In some embodiments, the aspartic protease is pepsin. In some embodiments, one protease maybe used to digest a protein. In some embodiments, more than one protease maybe used to digest a protein. In some embodiments, the digesting of step (v) is performed under conditions suitable for the protease to catalyze the cleavage of peptide bonds in the protein. Upon cleavage with a protease, the protein, which is covalently bound to the photo-tagged compound, is digested into constitutive peptides based on the specificity of the chosen protease or combination of proteases, thus providing a plurality of peptides comprising peptides that are covalently bound to the photo-tagged compound (i.e., conjugated peptides) and native peptides (i.e., peptides that are not covalently bound to the photo-tagged compound). [0142] In some embodiments, the step of identifying comprises performing mass spectrometry to identify the protein that is bound to the compound. Mass spectrometry (MS) has been used for the identification of protein-ligand interactions, see, for example, Sinz A . (2007) Investigation of Protein-Ligand Interactions by Mass Spectrometry. ChemMed Chem, 2, 425-431. In particular, peptide mixtures are generally separated before introduction into the mass spectrometer, such as through liquid chromatography (LC) or capillary electrophoresis (CE). In some embodiments, the mass spectrometry used in the step of identifying is intact mass spectrometry. Intact mass spectrometry may also be referred to as "native mass spectrometry", as this MS method generally involves preservation of the native protein or complex shape and structure. See, e.g., Doerr A . (2012) Mass spectrometry of intact protein complexes. Nature Methods, 10, doi:10. 1038/nmeth.2298. [0143] In some embodiments, when the method involves a digesting step, the identifying step comprises performing mass spectrometry to identify the peptides that are bound to the compound. In some embodiments, the mass spectrometry used in the identifying step is mass- independent mass spectrometry (MS). Without wishing to be bound by any particular theory, mass-independent MS generally involves the mass-independent assignment of peptides, which uses a pattern-searching algorithm to direct tandem MS analysis to isotopically labeled species (e.g., a compound comprising one or more isotopically labeled atoms). See, e.g.. Woo CM, etal (2015) Isotope-targeted glycoproteomics (IsoTaG): a mass-independent platform for intact N- and O-glycopeptide discovery and analysis. Nat Methods, 12(6), 561-567. Mass- independent MS can overcome traditional MS barriers in detection of low abundance species by enhancing the detection of the species of interest (e.g., the isotopically labeled species) even in a background of unmodified species (e.g., unmodified peptides that do not comprise an isotopically labeled atoms). Mass-independent mass spectrometry may also be referred to interchangeable as isotope-targeted mass spectrometry. [0144] In some embodiments, the identification of the peptide or protein species of interest (e.g., the peptide or protein conjugated to the photo-click tagged compound) can be enhanced by performing an enrichment step before the identifying step to increase the abundance (i.e., enrich) the conjugate (e.g., the protein conjugated to the photo-click tagged compound, the peptide conjugated to the photo-click tagged compound, the protein-protein complex conjugated by the amino acid analog, or a peptide of the first protein conjugated to a peptide of the second protein by the amino acid analog) present in the sample for analysis. Thus, in some embodiments, the method further comprises a step of enriching the conjugate formed when the photo-activated compound covalently binds to a protein. In some embodiments, the step of enriching is performed before the digesting step. In some embodiments, the step of enriching is performed after the digesting step. In some embodiments, the step of enriching is performed without digesting the protein before or after the enriching step. In some embodiments, the step of enriching comprises covalently attaching a label to the click chemistry handle of the photo-click tag. In some embodiments, the label comprises a click chemistry handle that can be conjugated (i.e., "clicked") to the click chemistry handle of the photo-click tag. In some embodiments, the label comprises an azide (N3) moiety. In some embodiments, the label is covalently attached to the click chemistry handle of the photo-click tag using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction conditions. The CuAAC is a click chemistry reaction that involves the copper-catalyzed reaction of an azide with an alkyne to form a 5-membered heteroatom ring. An exemplary scheme outlining a CuAAC reaction is shown below in Scheme ID.

While a CuAAC reaction requires an alkyne and an azide, a person of ordinary skill in the art is capable of determining appropriate reaction conditions for attaching a label to a click chemistry handle, wherein the label and the click chemistry handle do not comprise an azide or an alkene. See, e.g., Hein, CD et al (2008) Click Chemistry, a Powerful Tool for Pharmaceutical Sciences. Pkarm Res, 25, 2216-2230, which is incorporated by reference herein. [0145] In some embodiments, the label comprises an affinity tag. An affinity tag can be used to efficiently separate the protein or peptides covalently linked to the photo-click tagged compound (i.e., conjugated protein or conjugated peptides) from native proteins or peptides (i.e., proteins or peptides that are not covalently linked to the photo-click tagged compound). The term "affinity tag" refers to any moiety that can be used to separate a species of interest (e.g., a protein or peptide) from a complex mixture. Exemplary affinity tags include, but are not limited to, peptide tags (e.g., AviTag (GLNDIFEAQKIEWHE), Calmodulin-tag (KRRWKKNFIAVS AANRFKK SSSGAL), polyglutamate tag (EEEEEE), E-tag (GAPVPYPDPLEP ) FLAG-tag (DYKDDDDK), HA-tag (YPYDVPDYA), His-tag (5- 0 histidines, e.g., HHHHHH), Myc-tag (EQKLISEEDL), NE-tag (TKENPR S QEESYDDNES), S-tag (KETAAAKFERQHMDS), SBP-tag (MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP), Softag 1 (SLAELLNAGLGGS), Softag 3 (TQDPSRVG), Strep-tag (Strep-tag II: WSHPQFEK), TC tag (CCPGCC), Ty tag (EVHTNQDPLD), V5 tag (GKPIPNPLLGLDST), VSV-tag (YTDIEMNRLGK), Xpress tag (DLYDDDDK), and derivatives thereof, covalent peptide tags (e.g., Isopeptag (TDKDMTITFTNKKDAE), SpyTag (AHIVMVDAYKPTK), SnoopTag (KLGDIEFIKVNK), SnoopTagJr (KLGSIEFIKVNK), DogTag (DIPATYEFTDGKHYITNEPIPPK), and derivatives thereof), protein tags (e.g., BCCP (Biotin Carboxyl Carrier Protein), Glutathione-S-transferase-tag, Green fluorescent protein- tag, HaloTag, Maltose binding protein-tag, Nus-tag, Thioredoxin-tag, Fc-tag, Designed Intrinsically Disordered tags, chitin binding protein (CBP), thioredoxin (TRX), and derivatives thereof), biotin, avidin (e.g., streptavidin), carbohydrates (e.g., lectins), and glutathione. Affinity tags are often added to a species of interest (e.g., a protein or peptide) to facilitate separation, for example, using affinity chromatography, by taking advantage of the specific interaction between two moieties (e.g., antigen and antibody, enzyme and substrate, receptor and ligand, or protein and nucleic acid). In some embodiments, the affinity tag is biotin. In some embodiments, the label is of the formula:

[0146] In some embodiments, the method further comprises separating the protein or peptides covalently linked to the photo-click tagged compound, wherein the photo-click tagged compound is covalently attached to the label. In some embodiments, when the label comprises biotin, the conjugated protein or conjugated peptide can be separated from native proteins or peptides by streptavidin-coupled beads. Once the conjugated protein or conjugated peptide is captured by the interaction between the biotin of the label and the streptavidin of the beads and separated from the native proteins or peptides, the conjugated protein or conjugated peptide can be cleaved from the beads, for example, using acidic cleavage conditions, thereby releasing the conjugated protein or conjugated peptide and generating an enriched sample for identification of the protein or peptide covalently bound to the photo-click tag. Additional suitable labe /derivative-bead combinations will be apparent to those of skill in the art based on this disclosure and knowledge in the field, and are within the scope of this disclosure [0147] In some embodiments, the protein is present in a whole proteome. In some embodiments, the protein is present in vitro. For example, the methods can be performed on a sample consisting essentially of the protein of interest (e.g., the protein that binds to a small molecule of interest), such as in a purifi ed protein sample. The methods can also be performed on a sample comprising a mixture of proteins in a sample (e.g., a cell iysate). In some embodiments, the protein is present in a cell lysate. In some embodiments, the protein is present in vivo. In some embodiments, the protein is present in a cell. In some embodiments, the ceil is a mammalian (e.g., human) ceil. In some embodiments, the cell is a human cell. In some embodiments, the cell is a human cell derived from a subject with a disease (e.g., cancer).

EXAMPLES [0148] In order that the invention described herein may be more fully understood, the following examples are set forth. The examples described in this application are offered to illustrate the methods, compositions, and systems provided herein and are not to be construed in any way as limiting their scope.

Example 1-Small molecule interactome mapping by photo-affinity labeling (SIM-PAL) reveals binding site hotspots for the NSAIDs [0149] Many therapeutics elicit cell-type specific polypharmacology that may increase therapeutic efficacy or yield off target toxicity. However, direct observation of the structures that underpin the global molecular associations between the proteome and even common therapeutics, such as the non-steroidal anti-inflammatory drugs (NSAIDs), remain little understood. Presented here is a platform termed small molecule interactome mapping by photo-affinity labeling (SIM-PAL) and apply it to the in vivo characterization of the NSAID interactome to yield identification of specific binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, the NSAID interactome consisting of over 1000 enriched proteins was identified and nearly 200 conjugated peptides representing direct binding interactions in Jurkat and K562 cells were directly characterized. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κΒ) and novel interactions (e.g., AP-1, proteasome). These data further revealed a binding site hotspot on histones H2A and H2B where the three photo-NSAIDs, but not fragment-based small molecules, interacted. The binding interaction of the NSAIDs stabilized COX-2 and histone H2A by cellular thermal shift assay. Since protein-protein stabilization is a gain of function regulator}' mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-P AL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest. Introduction [0150] Polypharmacology, wherein one drug interacts with multiple protein targets, is a common phenomenon in drug discovery. Polypharmacology manifests in increased efficacy when properly exploited or tragic unanticipated off-target effects when not fully understood. Many pharmaceuticals in diverse therapeutic areas possess either known or uncharacterized polypharmacology, 1 such as the nonsteroidal anti-inflammatory drags (NSAIDs), 2 the immunomodulatory drugs or the opioids. 4 Proteomic differences across cell types are the basis for molecular interactions that culminate in an observed phenotype, 5 suggesting that with a map of the protein-ligand interaction network throughout the whole proteome, these polypharmacology outcomes may eventually be predicted. 6-7 [0151] A method to directly map the small molecule interactome has the potential to accelerate drug discovery by providing structural insight and instant validation of the binding interaction, yet such global characterization is rarely perfomied. Common analytical methods to structurally reveal small molecule binding sites, such as X-ray crystallography or NMR spectroscopy, are constrained to the measurement of stable interactions between a single compatible protein and small molecule pair in vitro. Global proteomic profiles are now commonly obtained using mass spectrometry (MS), and with a small molecule affinity purification strategy can be used to identify binding proteins. 8 However, the vast majority of proteomics studies stop short of obtaining direct structural evidence for the molecular interaction, due to inherent challenges in mapping the binding sites of a small molecule on the whole proteome. Small molecule interactions occur over a range of concentrations that require a general mechanism for capture and enrichment prior to MS analysis. The chemistry selected to capture the binding event must be rapid and general for unbiased covalent bond formation at the small molecule binding site. Yet, the demand for a general chemical strategy to covalentiy conjugate a small molecule locally to the protein interaction site poses great challenges to spectral assignment by database searching. Database searching methods are not adapted to the computational complexity yielded by amino acid residue-agnostic modifications to the whole proteome. Without the complexity of the whole proteome, binding sites of small molecules to defined protein isolates can be determined by application of photo-affinity labeling (PAL) to conjugate the small molecule to the protein prior to MS analysis. 9 [0152] Translation of MS-based binding site identification from a single protein to the whole proteome thus requires (1) a selective chemical workflow to isolate the conjugated peptide and (2) a targeted MS technique for confident characterization. PAL covalentiy conjugates small molecules to the proteome for stringent enrichment of interacting proteins. 10 Application of cleavable enrichment handles enables recovery of the small molecule- conjugated peptide.9 Critically, a targeted MS strategy, wherein unique isotopic markers are installed specifically to the small molecule conjugated peptide, provides an orthogonal handle for detection and validation that proves transformative during database assignment of

peptides carrying heterogeneous modifications by MS. 1 1 Recent strides have enabled the identification of fragment-based small molecule ligands to the whole proteome. 12 [0153] The knowledge gap caused by the lack of a small molecule interactome map extends to common pharmaceuticals like the nonsteroidal anti -inflammatory drugs (NSAIDs). The NSAIDs are potently suppress inflammation, pain, and fever and have been further explored as potential treatments for cancer2,13 and Alzheimer's disease. 14 NSAID mechanisms have been primarily characterized through inhibition of the enzymes cyclooxygenase-1 and 2 (C X- , COX-2, respectively). 15 Inhibition of COX-2, the primary cyclooxygenase involved in inflammation, prevents the production of prostaglandins, thereby reducing inflammation. However, a wealth of biomedical evidence points to broader COX-2-independent mechanisms of NSAIDs involved in anti-cancer activity for which a molecular basis remains poorly defined. 16 18 Prior studies suggest that specific NSAIDs inhibit the nuclear factor-κΒ (NF-KB) pathway 9 and caspases. 20 A detailed understanding of broader NSAID mechanisms is constrained by the absence of a global understanding of NSAID-protein interactions and their underlying structures. [0154] Herein, the development of a platform termed small molecule interactome mapping by photo-affinity labeling (SIM-PAL) and its application to the NSAIDs is reported. S M PAL is designed to directly characterize the protein interactions and binding site hotspots of a small molecule in a whole cell proteome using a PAL-based enrichment strategy coupled to isotope-targeted MS (Figure 12A . Our platform involves: (1) photo-conjugation of NSAID derivatives in cells, (2) enrichment and isotopic recoding of N SA D- abe ed peptides, and (3) isotope-targeted assignment of the conjugated peptides Photo-NSAID derivatives are effective reporters of NSAID binding sites with recombinant COX-2 and the global whole cell proteome, as shown herein. Photo-NSAJDs displayed overlapping protein interactions in Jurkat and K562 cell lines. By virtue of direct characterization of the conjugated peptide, we localized the photo-NSAIDs to a specific binding hotspot on the interface of histones H2A and H2B. Histone H2A was stabilized by interacting with the NSAIDs by cellular thermal shift assay. SIM-PAL revealed the precise binding interactions for the photo-NSAIDs via an approach that is readily translated to broad classes of small molecules.

Results Development of photo-NSAIDs as reporters of NSAID binding sites [0155] Three NSAIDs, naproxen (1), celecoxib (2), and indomethacin (3), were conjugated to diazirine-based photo-affinity labels ("photo-NSAIDs") to serve as reporters for NSAID binding sites (Figure 12B). These NSAIDs were selected for their different structure-activity relationship (SAR) between COX-1 and COX-2. 2 '22 Naproxen (1) is a nonselective COX-1 and COX-2 inhibitor, but is commonly employed for chronic use due to low rates of gastrointestinal side effects. 23 Celecoxib (2) is a selective COX-2 inhibitor developed by Pfizer, yet possesses off-target cardiovascular and gastrointestinal complications. 24 Indomethacin (3) is a member of the indole class of NSAIDs and possesses known COX-2 - independent anti-inflammatory mechanisms. 16 The design of photo-NSAIDs were based upon previous SAR studies 25,26 and the crystal structure between mouse COX-2 and indomethacin (3). During our studies, a crystal structure of a NSAID with human COX-2 was reported. 28 In addition to photo-NSAIDs 4-6, the tag 7 a structurally orthogonal photoglutarimide 8, and a celecoxib analog 9, was developed to assess selectivity of the binding site identification assay (Figure 26). [0156] All three photo-NSAIDs maintained COX-2 inhibition by ELISA (Figure 12B, Figures 16A-16D), although some variation in activity was observed. Photo-celecoxib (5) was the most potent ( C o = 36.6 nM) and photo-naproxen (4) was the least potent ( C o = 36.0 uM). All photo-NSAIDs possessed antiproliferative properties within 1.3-1.4-fold of their parent compound in Jurkat cells (Figures 17A-17D). Elimination of the sulfonamide from celecoxib (2) to give the analog 9 is known to reduce COX-2 inhibition' 6 and we found additional ly attenuated anti-proliferative activity of the analog 9 in activated Jurkat cell s (Figures 17A-17D). Furthermore, all photo-NSAIDs were competitively displaced from recombinant COX-2 by the native NSAID (Figure 13,4). COX-2 was separately incubated with each of the photo-NSAIDs with or without a 100-fold excess of the parent compound as a competitor. 10 The samples were photo-irradiated, tagged with the fiuorophore TAMRA- azide by copper-mediated azide alkyne cycloaddition (CuAAC), or click chemistry, and fluorescently visualized to reveal selective and reversible binding of COX-2 to the photo- NSAIDs. The tag 7 did not produce observable conjugation to COX-2 by fluorescence. Photo-NSAIDs possess known and transient binding sites with COX-2 [0157] Recombinant COX-2 was used to validate fragmentation patterns of conjugated NSAIDs to a protein and determine binding site selectivity for each of the photo-NSAIDs. Small molecule modification on a peptide may perturb MS fragmentation pathways in unexpected ways, rendering the spectra unable to be assigned by database searching. To evaluate this possibility, photo-NSAIDs (10 µΜ) were incubated with recombinant COX-2 for 30 minutes and photo-irradiated. The irradiated samples were appended to the cleavable biotin azide probe 10 to simulate the conjugated species ultimately observed after enrichment (Figure 2C The probe 0 is a multifunctional probe developed to possess a biotin affinity enrichment handle, an acid-labile diphenylsilane, and a stable isotope-coded azidoacetate for click chemistry and isotope-targeted MS. We previously established the compatibility of a similar cleavable probe scaffold in targeted MS experiments. Following click chemistry, the samples were trypsin-digested and the probe was cleaved in situ (2% formic acid). The resulting peptides were analyzed by LC-MS/MS. MS data was searched by SEQIJEST and Byonic against recombinant COX-2 with the photo-NSAID as a modification on any amino acid (Table 2). Due to the nature of photochemical conjugation, a binding site will be represented by multiple conjugated peptide structures and potentially multiple surrounding peptides i the MS data. All peptide spectral matches (PSMs) assigned to a conjugated peptide were manually validated. [0158] Photo-NSAIDs were readily assigned by database searching. Manual inspection of these PSMs indicated that in the case the photo-NSAIDs 4-6, no irregular fragmentation pathways were observed. As expected, at a consistent dose of 10 µΜ across all photo- NSAIDs, photo-celecoxib (5) possessed the highest number of observed conjugated peptides (seven conjugated peptides from 14 PSMs), including within the active site of COX-2. Analysis of COX-2 treated by photonaproxen (4) and photo-indomethacin (6) revealed six conjugated peptides across 9 PSMs and eight PSMs, respectively (Table 2). By contrast, the tag 7 was found conjugated to one peptide, which was not marked by the photo-NSAIDs. Within each peptide, the specific conjugation site localized to a range of 2-4 amino acid residues that reflect the specificity of the photochemical conjugation event. [0159 The photo-NSAIDs, the parent compounds, and the tag 7 were structurally minimized [Gaussian 16, basis set: F 3-21g(d)] and individually docked in the crystal structure of human COX-2 (PDB: 5 R).28 Docking was performed using Patchdock, a molecular docking algorithm based on shape complementarity using rigid structures. 30 Structures with the lowest desolvation energy or highest interface area size docked the photo-NSAID or parent compound to the same interaction site, although the orientations within each pair of compounds differed {Figures 13B 13D). The docked structure of photo-naproxen (4, red), photo-celecoxib (5, green), and photo-indomethacin (6, yellow) overlaid with their respective parent compound (blue). Conjugated amino acid residues within 5 A of the docked photo- NSAID are highlighted in Figures 13B 1 D . The orientation of each of the photo-NSAIDs positioned the diazirine in close proximity to one or two specific amino acids on a conjugated peptide observed by MS. Other marked residues were located on solvent exposed areas of the protein. As photochemistry captures dynamic processes and the photochemical tag is structurally flexible, the additional conjugation events on recombinant COX-2 may represent transient interactions with COX-2 in vitro, which may not be observed in cellulo. The tag 7 was additionally docked and, in combination with the observed M S data, was shown to transiently bind to an orthogonal region of COX-2 {Figure 13E . No conjugated peptides from amino acids near to the canonical binding site were observed. Characterization of the NSAID interactome in Jurkat and K562 cells [0160] Confident that photo-NSAIDs were producing defined linkages with COX-2 that recapitulated NSAID activity, we next sought to characterize global NSAID interactions within the whole ceil proteome. Photo-NSAIDs, the tag 7, and the photo-glutarimide 8 were added to activated Jurkat T cells as a model system for inflammation. Small molecule dose- dependent and photo-irradiation-dependent labeling of the proteome peaked at 250 µΜ . Competitive displacement of the tightest COX-2 binder photo-celecoxib (5) by the parent compound occurred at a 1:10 molar ratio {Figures 18A-18C). Jurkat cells were stimulated

with phorbol myristyl acetate and ionomycin for 18 hours prior to photo-NSAID exposure. 3 1 The stimulated Jurkat cells were exposed to each compound (250 uM, 1 hour) and photo- irradiated in situ to conjugate the small molecule to the proteome. The resulting NSAID- conjugated proteins were enriched using the probe 10 in a biotin-dependent manner {Figure 19). COX-2 from Jurkat cells was enriched by photo-NSAIDs and this enrichment was abrogated by competition with the parent compound, as indicated by Western blot (Figure 2OA). Cellular thermal shift assay, an orthogonal mechanism to validate protein-ligand

interactions, 32 showed that COX-2 was stabilized by celecoxib (2) and photo-celecoxib (5) by over 0 °C relative to the tag 7 (Figure 20B-C). [0161] The enriched proteomes were digested with trypsin and the released peptides were analyzed by LC-MS/MS on an Orbitrap Fusion Tribrid with collision induced dissociation (CID) and higher energy CID (HCD) fragmentation modes. M S data were assigned by SEQUEST HT Two biological replicates were collected for each of the photo-NSAIDs that displayed high reproducibility across the enriched proteome (>60%) and protein abundance (Figure A) Using PSM-based label free quantification, J proteins that were greater than 2- fold enriched and statistically significant (t-test, p-value < 0.05) were considered selectively enriched by the photo-NSAID relative to the control tag 7 (Figure MA). This analysis yielded approximately 700 proteins significantly enriched by at least one of the photo- NSAIDs (Table 3). High proteomic overlap amongst photo-NSAIDs, but not negative controls 7 and 8, was observed. Across each of the three compounds, at least 40% of the identified photo-NSAID-binding proteins were enriched by ail three photo-NSAIDs and 53% of the proteins were enriched by at least two photo-NSAIDs (f igure 14B). By comparison, 140 proteins that were statistically enriched by any photo-NSAID were also enriched by the photoglutarimide 8 (24%). [0162] Jurkat cells were initially dosed with a concentration of 250 µΜ of each photo- NSAID to maximize downstream observation of conjugated peptides by MS. Although

naproxen (1) enters blood plasma at concentrations that surpass 250 µΜ,34 our C o data against Jurkat cells showed a range of 23-216 µΜ across the NSAIDs and their derivatives Figure 17A-17D). We thus examined the NSAID interactome at 50 µΜ and identified 260 proteins enriched by the three photo-NSAIDs and not by the tag 7 (Table 4). At 50 µΜ the proteomic overlap between the photo-NSAIDs was lower, indicative of higher selectivity between the molecular stnictures (Figure S6B). A majority of proteins identified at 50 µΜ were likewise identified at 250 µΜ for each photo-NSAID (86-92%). The celecoxib analog 9 (50 µΜ) was additionally tested in activated Jurkat cells and displayed moderate proteomic overlap with photo-celecoxib (5) (Figure 21C). [0163] To determine the generality of these observations, photo-NSAIDs were additionally tested against K562 cells, a human chronic myeloid leukemia cell line. Several lines of evidence point to NSAID-dependent inhibition and apoptosis of K562 cells. 35 A total of 513 proteins were significantly enriched across two biological replicates from K562 ceils, of which 42% of the proteins were enriched by at least two of the three photo-NSAIDs {Figures 22 and 23). Significantly enriched proteins from K562 ceils possessed a moderate overlap with proteins from Jurkat cells (206 proteins), indicating a high degree of specificity across cell lines {Figure 14C). In sum, a total of 1034 proteins were enriched from Jurkat and K 562 ceils by photo-NSAIDs (Table 3). [0164] Photo-NSAIDs interacted with proteins distributed throughout the cell (Figure 14D).

Approximately two thirds of the NSAID interactome localized to the nucleus and cytoplasm. Photo-NSAIDs additionally captured proteins annotated as localized to the mitochondria

(10%), endoplasmic reticulum and Goigi ( 11%), and membrane or secreted proteins (10%). These data are a close refl ection of the natural distribution of proteins throughout the cell 36 Only 30% of these proteins were previously annotated as interacting with a small molecule, let alone one of the NSAIDs (BindingDB, ChEMBL, DrugBank). This gap may be in part due to the broader range of interactions captured by photo-conjugation as compared to existing target identification strategies. Comparison of photo-NS AID interactions with proteomics profiles derived from fragment-based small molecules 12 revealed a 60% overlap. Thus, photo-NSAIDs possess a protein interaction profile that is specific to molecular structure and cell type. These data point to a broader range of molecular interactions that remain to be revealed by the reported profiling approach. [0165] In line with evidence for capture of a broader range of associated proteins, a number of protein complexes were selectively enriched. Comparison of enriched proteins to CORUM37 revealed that NF-κΒ subunits (NF , NFKB2) in complex with the inhibitor of NF-KB (IKKA) are directly interacting with the photo-NSAIDs, confirming their known inhibition of the NF-κΒ pathway 2 and was revalidated for celecoxib (2) and photo-celecoxib (5) via a NF-κΒ luciferase reporter assay {Figures 14E and 24). Additional protein complexes that were nearly completely enriched include the proteasome and the adaptor protein complex

2 {Figure 14E). These proteins may have existed as complexes leading to photo- NSAID conjugation by virtue of proximity, indicative of a binding site hotspot for the photo-NSAIDs within specific families of proteins, or were enriched due to associative protein interactions. While protein complexes can be enriched through associative protein-protein interactions, our use of strong dissociative detergents to prepare cell lysates (1% Rapigest, sonication) does not typically lead to observation of protein complexes following enrichment. Direct photo-NSAID interaction mapping reveals binding site hotspots [0166] Following tryptic digestion of the photo-NSAID proteome, the probe 10 was acid cleaved to release the conjugated peptides from the enrichment media for separate isolation. The conjugated peptides were analyzed by application of mass-independent MS. A unique

isotopic signature was embedded to the probe 10 using a carbon- 3-derived stable isotope

ratio of :3 over [M:M+2] spacing to perform mass-independent MS. During click chemistry, the unique isotopic signature was exclusively transferred to the photo-NSAIDs conjugated to the proteome. The isotopic signature is therefore only found on small molecule-conjugated peptides and is used during mass-independent MS to overcome traditional MS barriers in detection of low abundance species and validation of modified peptides against a background of unmodified peptides. During data collection, the isotopicaliy receded species is immediately recognizable by full scan MS and may be selected for fragmentation by use of an inclusion t. "' This selection process increases the fraction of isotopicaliy receded, small molecule-conjugated peptides selected for fragmentation. 11 [0167] More critically, the isotope signature played a crucial role in manual validation of database search assignments due to the ambiguity of the amino acid modification site. Database searching was performed against the SwissProt human protein database with each of the photo-NSAIDs as a modification on any amino acid residue. Small molecule conjugation to any amino acid drastically increases the size of the protein database. For example, a single modification increases the size of the fully tryptic human protein database by 60-fold, while two modifications increase the database size by 1000-fold. This exponential increase in the tryptic peptide database leads to a breakdown in false discovery rate (FDR). 40 Thus, a two-tier validation process was used for confident assignment of conjugated peptides. First, modified peptides at 5% FDR were filtered based on visual inspection of the MS2 spectral assignment. Second, each of the precursor spectra was individually validated for the isotopic signature in the MSI. Based on this analysis, 575 PSMs, corresponding to 194 individual conjugated peptides, were characterized across the photo-NSAIDs, tag 7, and photo-glutarimide 8 (Table 5). The top ten most frequently observed conjugated peptides are displayed in Table I .

Table 1. Selected conjugated peptides observed with high PSM frequency across photo-

NSAIDs, the tag 7 and the photo-glutarimide 8 . Presented data is in aggregate across Jurkat

and K562 ceils. For the full dataset, see Table 5.

Count of PSMs Conjugated Peptide Protein (Gene) 4 5 6 7 8

Histone H2B type 1- 1 AMGIMNSFVNDIFER (SEQ ID NO: A ) 4 1 12 1 K (HIST 1H2BK) VGAGAPVYLAAVLEYLTAEILELAGNAAR Histone H2A type 2- 2 8 28 9 (SEQ ID NO: A2) B (HIST2H2AB) Actio, cytoplasmic 1 3 VAPEEHPVLLTEAPLNPK (SEQ ID NO: A3) 4 3 (ACTB) VGAGAPVYMAAVLEYLTAEILELAGNAAR Histone H2A type 2- 4 2 (SEQ ID NO: A4) A (HIST2H2AA3) Nucleophosmin 5 MSVQPTVSLGGFEITPPWLR (SEQ ID NO: A3) 7 \ (NPMl) X-ray repair cross- 6 NLEALALDLMEPEQAVDLTLPK (SEQ ID NO: A.6) complementing 6 7 3 I 2 (XRCC6) Tubulin alpha- 1A IHFPLATYAPVISAEK (SEQ ID NO: A7) 1 chain (TUBA 3A) VGAGAPVYLAAVLEYLTAEILELAGNAARDNKK Histone H2A type 2- (SEQ D NO: A8) B (H1ST1H2AB) Histone H4 9 ISGLIYEETR (SEQ ID NO: A9) 2 10 1 (HIST1H4A) Elongation factor 1- 0 VETGVLKPGMWTFAPVNVTTEVK (SEQ ID NO: A ) 5 n alpha 1 (EEFIAI) Cathepsin D i AIGAVPLIQGEYMIPCEK (SEQ ID NO: Al l ) 4 3 (CTSD)

[0168] The individual peptides derived from a total of 150 proteins, of which over 90% of the proteins were greater than two-fold enriched, but did not necessarily pass statistical significance, by at least one of the photo-NSAIDs than by the tag 7 . A number of isotopically-coded species that were either not selected or not confidently assigned by SEQUEST were also observed. Detection of enriched conjugated species using a pattern searching algorithm39 revealed nearly 1000 isotopically coded precursor ions in the MSI spectra across our photo-NSAID conjugated peptide data. [0169] The observed interaction frequency and overlap was specific to the small molecule. Photo-eelecoxib (5) and photonaproxen (4) represented the bulk of the identified interactions and were found conjugated to 93 and 85 peptides, respectively. Photo-indomethacin (6) was conjugated to 34 peptides in total. A degree of overlap between the photo-NSAID conjugated peptides was observed, where 30 peptides were identified by at least two of the three photo- NSAIDs. Of these, a single conjugated peptide on Ku70, a member of the DNA repair pathway, was observed by two photo-NSAIDs, the tag 7 and photo-glutarimide 8 (entry 6,

Table 1). The remaining 14 conjugated peptides detected by the tag 7 and nine conjugated peptides from the photo-glutarimide 8 were detected exclusively by that compound. [0170] We found a significant number of PSMs assigned to NSAID-conjugated histone peptides (Figure 15A, Figure 25). All directly observed histone interactions were highly interconnected and imply significantly upregulated conjugation of histone complexes by the photo-NSAIDs (Figure 15B). These proteins were enriched in photo-NSAID proteomic data as compared to the tag 7, but were not considered statistically significant. In particular, two peptides from histone H2A and histone H2B were primarily detected. The histone H2B peptide was detected in a total of 54 PSMs across our datasets, predominantly by photo-

naproxen (4, entry 1, Table 1). Histone H2A type 2-A and type 2-B were detected in a total of 62 and 19 PSMs, respectively (entries 2, 4, and 8, Table 1), predominantly in Jurkat cells. These PSMs related to peptides conjugated to photo-celecoxib (5), followed by photonaproxen (4) and to a lesser degree photo-indomethacin (6). By virtue of directly observing the conjugated peptide, photo-NSAIDs were mapped to a specific binding site hotspot around these two peptides, which are in close proximity in structures of the nucleosome (Figure 15C) Conjugated peptides from nucleophosmin and elongation factor 1-alpha 1 (entries 6 and 10, Table 1) were also observed. [0171] Validation of SIM-PAL by competition assay revealed that binding of all three photo- NSAIDs with histone H2A and H2B was competitively exchanged with the parent compound by Western blot (Figure 15D). The interaction of photo-NSAIDs with NF-κΒ p65 was additionally completely displaced by the parent compound. Selective photo-conjugation and partial competition was observed when probing for Ku70 or nucleophosmin. The tag 7 and photo-NSAIDs labeled elongation factor 1-alpha 1 and rho GDP-dissociation inhibitor 2 similarly, although partial competition was still observed in some cases (data not shown). Cellular thermal shift assay in Jurkat cells showed stabilization of histone H2A by all three NSAIDs and the celecoxib analog 9 relative to the tag 7 by 10-15 °C (Figure 15E). Photo naproxen (4) and photo-celecoxib (5) also stabilized histone H2A, while photo-indomethacin

(6) did not. These data are in line with the PSM frequency in Table 1. Characterization of these binding sites for biological function will be pursued. Discussion [0172] The development and application of SIM-PAL to enable characterization of the small molecule interactome and direct binding interactions was described (Figure 12A). SIM-PAL provides several key advantages, including: (I) instant validation of the interaction by virtue of direct observation, (2) measurement of a range of interactions between transient and highly specific binding events, and (3) structural information about the binding site and the small molecule structure. These advantages are highlighted by our analysis of three NSAIDs for their binding sites with a single protein (COX-2) and against the whole proteome from Jurkat and K562 cells. [0173] We applied SIM-PAL to three NSAIDs, naproxen (1), celecoxib (2), and indomethacin (3), due to their different structures yet similar anti-inflammatory effects. Variation in their off-target toxicity and the affected COX-2-independent anti-inflammatory pathways has been reported with a limited molecular basis for these effects. For example, celecoxib was the result of a medicinal chemistry optimization for COX-2 selectivity relative to COX-1,22 yet additional COX-2 independent mechanisms have been subsequently reported 8 To illuminate the molecular driving force behind NSAID biology, we developed a set of photo-NSAIDs (4-6, Figure 12B) that recapitulated the activity of the parent compounds and demonstrated their direct binding interaction with COX-2 (Figures 13A- 3E . Due to the dynamic nature of PAL, we identified additional transient interactions with COX-2 in vitro and the broader proteome in cellulo. These data report on access and molecular recognition of the compounds to the proteome and afford a structural basis for further functional analysis or protein degradation strategies.42 A systematic study of the kinetics of PAL will provide concrete measurement of the range of transient interactions observable by SIM-PAL. [0174] Application of the photo-activated compounds 4-8 to stimulated Jurkat and K562 ceils revealed specific protein interactions that were more homologous across the three photo- NSAIDs than with the tag 7 or the photo-glutarimide 8 . The photo-NSAID interactome revealed entire protein complexes of both known and novel interactions. For example, specific proteins in the NF-κΒ pathway are now identified as direct interactors (figures 14E and 24). Enrichment of several protein complexes also indicates that the photo-conjugation event is dynamic and highly specific to the local environment of the small molecule at the time of activation. Novel interactions with the proteasome and the adaptor protein complex 2 were also notable. These results provide insight to the molecular interactions within the proteome generated by the NSAIDs, which may or may not possess direct biological function. Selection of proteins for follow up functional studies may be based on existing biological relevance, relative abundance, or dose dependence. Further studies may reveal functional relevance and the basis for some of the poorly-understood biological effects of NSAIDs. [0175] We elected to evaluate a specific conjugation event that was observed on an interface between histone H2A and H2B in the nucleosome due to the high frequency of PSMs in our MS data. The two peptides are within 6 A of each other in a crystal structure of the nucleosome, indicative of a binding site hotspot recognized by the photo-NSAIDs 4 1 While all three photo-NSAIDs were able to conjugate these peptides, photonaproxen (4) conjugation to histone H2B was observed the most frequently, while conjugation of photo-ceiecoxib (5) was most frequently observed conjugated to histone H2A. Comparison of these data to fragment-based small molecule interaction sites revealed that a diazirine-tagged coumarin, most structurally similar to photo-naproxen (4), likewise conjugated a similar peptide from histone H2AZ. 12 The interaction of photo-NSAIDs with histones was competitively displaced by the parent compound by Western blot (Figtire 15D). These data point to the existence of a binding site hotspot i the nucleosome. Although functional relevance cannot be inferred simply due to observation of an interaction, celecoxib (2) and photo-ceiecoxib (5) stabilized histone H2Aby cellular thermal shift assay (Figure 15E). Stabilization of protein compl exes leading to downstream signaling changes is reminiscent of other immunomodulators, including cyclosporin, FK506, and rapamycin, 43 and the immunomodulatory drug lenalidomide. 44, The photo-NSAIDs reported here are validated probes that may be applied to additional biological studies. [0176] While the photo-NSAIDs interacted with and stabilized COX-2 in cellulo, COX-2 was only observed in PSMs at a FDR >1% that were thus removed from the final dataset (Table 3). Furthermore, conjugated peptides from only a fraction of the enriched proteins were identified. These detection differences reflect the increased challenge in seeking to perform site-specific identification of a single conjugated peptide as opposed to protein identification that may derive from multiple peptides from the same protein. Deeper analysis of the NSAID interactome may be obtained by increasing protein inputs, increasing chromatographic separation, application of additional fragmentation methods, or use of a second protease (e.g., chymotrypsin). [0177] SIM-PAL represents the culmination of advances in chemical enrichment strategies coupled to MS technology and a computational pattern searching algorithm to lay the groundwork for rapid progress in direct structural characterization of small molecule interactions within the whole proteome. Recent work in profiling small molecule modification sites has begun to expand the number of interactions that are known to occur throughout the proteome and enable a deeper understanding of the molecular underpinnings of polypharmacology. SIM-PAL revealed the global interaction map for the three NSAIDs profiled and is readily translated to other clinically relevant agents. For example, the immunomodulatory drugs have widely established plunpotent activity and the mechanism of action is only partly understood.' Alternatively, metformin is widely used to treat diabetes with little understanding of the underlying mechanism. 46 SIM-PAL is poised for broad application to bioactive small molecules for identification of proteomic interactions using an unbiased whole cell assay.

Table 2 . Summary of conjugated peptides representative of binding sites of photo-NSAIDs o recombinant COX-2. Amino acids that were identified as the conjugation site by SEQUEST HT searching are denoted in bold lowercase letter. COX-2 tryptic digests were analyzed on an Orbitrap Elite and assigned to tryptic or semi-tryptic peptides using SEQUEST HT. 165 QLPDSNEIVeK 908.90686 18 16.80644 8 16.81 459

165 QLPDSNEIVeK 835.87292 1670.73857 1670.73422

166 QLPDSNEIVEk 907.9051 18 14.80303 8 14.79894

248 YQIIDGEMyPPTVK 1099.9956 2 198.98393 2 198.98609

248 YQIIDGEMyPPTVK 1026.9542 2052.901 7 2052.90572

320 LILIGeTIKIVIEDYV 973.80646 291 9.40482 29 9.40067

446 yQSFNEYR 826.32996 1651 .65264 1651 .65697

446 yQSFNEYR 753.28943 1505.571 8 1505.5766

455 rFMLKPYESFEELTGEKEMSA 979.75653 2937.25504 2937.27554 GCPFTSfSVPDPEL! KTVTi NASSSRS 566 866.58209 4328.881 35 4328.89089 GLDD

74 LFLKPTPNTvHY!LTHFK 921 .8 8 1 2763.43998 2763.45766

93 ILTHFKGFWNWNNIPfLR 921 .81226 2763.42221 2763.43652

113 pPTYNADYGYK 941 .9 199 1882.81 67 1882.8201 9

339 LIL!GETIK!V!EDYVQHLsGYHFKLKF 901 .471 86 4503.33021 4503.32663 photo- indomethaein 343 V!EDYVQHLSGYHfK 761 .69812 2283.07981 2283.06763

423 SFTRQIAGRVAGgR 962.49585 1923.98442 1923.97434

586 TVTINASSSRs 785.871 28 1570.73528 1570.73031

597 SGLDD!NPTVLS 852.92023 1704.8331 1704.82863 Table 3 . Li e indicated compound (250 µΜ) at 1% FDR The fold change ratio and NSAF calculation to determine statistically significant enrichment are displayed.

1-acyl-sn-glycerol-3-pbosphate acyliransferase alpha (EC 2.3.1 .51) (1- acylg!ycero!-3-phospbate O-acyltransferase 1) Q99943 AGPAT1 283 FALSE FALSE FALSE FALSE FALSE TRUE (1-AGP acyitransferase 1) ( 1-AG PAT 1) (Lysophosphatidic acid acyitransferase alpha) (LPAAT-aipha) (Protein G15) 1-acyl-sn-glycerol-3-phosphate acyitransferase epsilon (EC 2.3.1 .51) (1- acylglyceroi-3-phosphate O-acyitransferase 5) Q9NUQ2 AGPATS 364 FALSE TRUE FALSE FALSE FALSE FALSE (1-AGP acyitransferase 5) ( 1-AG PAT 5) (Lysophosphatidic acid acyitransferase epsilon) (LPAAT-epsiion) 1-phosphatidyiinositol 4,5-bisphosphate phosphodiesterase beta-3 (EC 3.1 .4.1 1) QQ1970 PLCB3 1234 FALSE FALSE FALSE FALSE FALSE FALSE (Phosphoinositide phospholipase C-beta-3) (Phosphoiipase C-beta-3) (PLC-beta-3)

10 kDa heat shock protein, mitochondrial P616Q4 HSPE1 (Hsp10) (10 kDa chaperonin) (Chaperonin 10) 102 FALSE FALSE FALSE FALSE FALSE FALSE (CPN10) (Early-pregnancy factor) (EPF)

116 kDa U5 small nuclear ribonucleoprotein component (Elongation factor Tu GTP-bindinc Q15029 EFTUD2 domain-containing protein 2) (SNU1 14 972 TRUE TRUE TRUE FALSE FALSE FALSE homoiog) (hSNU1 14) (U5 snRNP-specific protein, 116 kDa) (U5-1 16 kDa) 4 kDa phosphohistidine phosphatase (EC 3.9.1 .3) (Phosphohistidine phosphatase 1) Q9NRX4 ΡΗΡΤ1 125 FALSE FALSE FALSE FALSE FALSE FALSE (PHPT1) (Protein histidine phosphatase) (PHP) (Protein janus-A homolog)

14-3-3 protein beta/alpha (Protein 1054) (Protein kinase C inhibitor protein 1) (KCIP-1) Ρ31946 YWHAB 246 FALSE FALSE FALSE FALSE FALSE FALSE [Cleaved into: 14-3-3 protein beta/alpha, N- terminally processed] Ρ62258 YWHAE 14-3-3 protein epsilon (14-3-3E) 255 FALSE FALSE FALSE FALSE FALSE FALSE Q04917 YWHAH 14-3-3 protein eta (Protein AS1) 46 FALSE FALSE FALSE TRUE TRUE TRUE 14-3-3 protein gamma (Protein kinase C Ρ61981 YWHAG inhibitor protein 1) (KCIP-1) [Cleaved into: 14- 247 FALSE FALSE FALSE FALSE FALSE FALSE 3-3 protein gamma, N-terminally processed] 14-3-3 protein sigma (Epithelial cell marker Ρ31947 SFN 248 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) (Stratifin) 14-3-3 protein theta (14-3-3 protein T-cell) (14- Ρ27348 YWHAG 245 FALSE FALSE FALSE FALSE FALSE FALSE 3-3 protein tau) (Protein HS1) 14-3-3 protein zeta/delta (Protein kinase C Ρ83104 YWHAZ 245 FALSE FALSE FALSE FALSE FALSE FALSE inhibitor protein 1) (KCIP-1) 2-oxoglutarate dehydrogenase, mitochondriai (EC 1.2.4.2) (2-oxoglutarate dehydrogenase Q02218 OGDH 1023 FALSE FALSE FALSE TRUE FALSE TRUE complex component E1) (OGDC-E1) (Alpha- ketogiutarate dehydrogenase)

2,4-dienoy!-CoA reductase, mitochondrial (EC 1.3.1 .34) (2,4-dienoyi-CoA reductase Q16698 DECR1 [NADPH]) (4-enoyl-CoA reductase [NADPH]) 335 FALSE FALSE FALSE FALSE FALSE FALSE (Short chain dehydrogenase/reductase family 18C member 1)

2',3'-cyc!ic-nucleotide 3'-phosphodiesterase P09543 CNP 421 FALSE FALSE FALSE TRUE TRUE TRUE (CNP) (CNPase) (EC 3.1 .4.37) 2',5'-phosphodiesterase 12 (2'-PDE) (2-PDE) Q6L8Q7 PDE12 (EC 3.1 .4 -) (Mitochondrial deadenylase) (EC 609 FALSE FALSE FALSE FALSE FALSE TRUE 3.1 .13.4) 26S proteasome regulatory subunit 10B (26S proteasome AAA-ATPase subunit RPT4) P62333 PSMC6 389 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome 26S subunit ATPase 6) (Proteasome subunii p42) 26S proteasome regulatory subunit 4 (P26s4)

P62191 PS C1 (26S proteasome AAA-ATPase subunit RPT2) F L3 Ε AL Ξ F L3 Ε F LS Ε FAL Ξ FAL3 EE (Proteasome 26S subunii ATPase 1) 26S proteasome regulatory subunit 6A (26S proteasome AAA-ATPase subunii RPT5) P17980 PS C3 (Proteasome 26S subunit ATPase 3) 439 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome subunit P50) (Tat-binding protein 1) (TBP-1 ) 26S proteasome regulatory subunit 6B (26S proteasome AAA-ATPase subunit RPT3) P43686 PS C4 (MB67-interacting protein) (MIP224) 418 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome 26S subunit ATPase 4) (Tat- binding protein 7) (TBP-7) 26S proteasome regulatory subunit 7 (26S proteasome AAA-ATPase subunit RPT1) P35998 PS C2 433 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome 26S subunit ATPase 2) (Protein MSS1 ) 26S proteasome regulatory subunit 8 (26S proteasome AAA-ATPase subunit RPT6) (Proteasome 26S subunit ATPase 5) P62195 PS C5 406 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome subunit p45) (Thyroid hormone receptor-interacting protein 1) (TRI P 1) (P45/SUG) 26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit Q99460 PS D1 3 FALSE FALSE FALSE FALSE FALSE FALSE RPN2) (26S proteasome regulatory subunit S 1) (26S proteasome subunit p 12 ) 26S proteasome non-ATPase regulatory 075832 PSMD10 subunit 10 (26S proteasome regulatory 226 FALSE FALSE FALSE FALSE FALSE FALSE subunit p28) (Gankyrin) (p28(GANK)) 26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory 000231 PS D 1 subunit RPN6) (26S proteasome regulatory 422 FALSE FALSE FALSE TRUE FALSE FALSE subunit S9) (26S proteasome regulatory subunit p44.5) 26S proteasome non-ATPase regulatory subunit 2 (26S proteasome regulatory 000232 PSMD12 456 FALSE FALSE FALSE FALSE FALSE FALSE subunit RPN5) (26S proteasome regulatory subunit p55) 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome regulatory Q9UN 6 PS D13 subunit RPN9) (26S proteasome regulatory 376 FALSE FALSE FALSE FALSE FALSE FALSE subunit S 1) (26S proteasome regulatory subunit p40.5) 26S proteasome non-ATPase regulatory subunit 14 (EC 3.4.19 -) (26S proteasome 000487 PS D14 310 FALSE FALSE FALSE FALSE FALSE FALSE regulatory subunit RPN1 1) (26S proteasome- associated PAD1 homoiog 1) 26S proteasome non-ATPase regulatory subunit 2 (26S proteasome regulatory subunit RPN1) (26S proteasome regulatory subunit Q13200 PS D2 908 FALSE FALSE FALSE FALSE FALSE FALSE S2) (26S proteasome subunit p97) (Protein 55.1 1) (Tumor necrosis factor type 1 receptor- associated protein 2)

26S proteasome non-ATPase regulatory subunit 3 (28S proteasome regulatory subunit 043242 PSMD3 534 FALSE FALSE FALSE FALSE FALSE FALSE RPN3) (26S proteasome regulatory subunit S3) (Proteasome subunit p58) 26S proteasome non-ATPase regulatory subunit 4 (26S proteasome regulatory subunit P55036 PSMD4 RPN10) (26S proteasome regulatory subunit 377 FALSE FALSE FALSE FALSE FALSE FALSE S5A) (Antisecretory factor 1) (AF) (ASF) (Multiubiquitin chain-binding protein) 26S proteasome non-ATPase regulatory Q16401 PSMD5 subunit 5 (26S protease subunit S5 basic) 504 TRUE TRUE TRUE FALSE FALSE FALSE (26S proteasome subunit S5B) 26S proteasome non-ATPase regulatory subunit 6 (26S proteasome regulatory subunit RPN7) (26S proteasome regulatory subunit Q15008 PS D6 S10) (Breast cancer-associated protein SGA- 389 FALSE FALSE FALSE TRUE TRUE FALSE 113 ) (Phosphonoformate immuno- associated protein 4) (Proteasome regulatory particle subunit p44S10) (p42A) 26S proteasome non-ATPase regulatory -4 subunit 7 (26S proteasome regulatory subunit P51665 PS D7 RPN8) (26S proteasome regulatory subunit 324 FALSE TRUE FALSE FALSE FALSE FALSE S12) ( ov34 protein homolog) (Proteasome subunit p40) 26S proteasome non-ATPase regulatory subunit 8 (26S proteasome regulatory subunit P48556 S D8 350 TRUE TRUE FALSE TRUE TRUE FALSE RPN12) (26S proteasome regulatory subunit S14) (p31) 26S proteasome non-ATPase regulatory 000233 PS D9 subunit 9 (26S proteasome regulatory subunit FALSE FALSE FALSE FALSE FALSE FALSE p27) 28 kDa heat- and acid-stable phosphoprotein Q13442 PDAP1 (PDGF-associated protein) (PAP) (PDGFA- 181 FALSE FALSE FALSE FALSE FALSE FALSE associated protein 1) (PAP1)

28S r boso a protein S10, mitochondrial P82664 RPS 0 (MRP-S10) (S10mt) (Mitochondrial small 2 1 FALSE FALSE FALSE FALSE FALSE FALSE ribosomal subunit protein uS10m) 28S ribosomai protein S 7, mitochondrial Q9Y2R5 MRPS17 (MRP-SI 7) (S17mt) (Mitochondrial small 130 FALSE TRUE FALSE FALSE TRUE FALSE ribosoma! subunit protein uS17m) 28S ribosomai protein S27, mitochondrial Q92552 MRPS27 (MRP-S27) (S27mt) (Mitochondrial small 414 TRUE FALSE FALSE FALSE TRUE FALSE ribosomai subunit protein mS27)

28S ribosomai protein S29, mitochondrial (MRP-S29) (S29mt) (Death-associated protein P51398 DAPS 3) (DAP-3) (Ionizing radiation resistance 398 TRUE FALSE FALSE FALSE FALSE FALSE conferring protein) (Mitochondrial small ribosomai subunit protein mS29)

39S ribosomai protein S30, mitochondrial (MRP-S30) (S30mt) (Mitochondrial large Q9NP92 MRPS30 ribosoma! subunit protein mL85) 439 FALSE FALSE FALSE FALSE FALSE FALSE (Mitochondrial large ribosoma! subunit protein mS30) (Programmed cell death protein 9)

28S ribosoma! protein S31, mitochondrial (MRP-S31) (S31mt) (Imogen 38) Q92665 1RPS31 395 FALSE TRUE FALSE FALSE FALSE FALSE (Mitochondrial small ribosomai subunit protein mS31) 28S ribosomai protein S35, mitochondrial (MRP-S35) (S35mt) (28S ribosomai protein P82673 MRPS35 S28, mitochondrial) (MRP-S28) (S28mt) 323 FALSE FALSE FALSE FALSE FALSE FALSE (Mitochondrial small ribosomai subunit protein mS35) 28S ribosoma! protein S9, mitochondrial (MRP- P82933 MRPS9 S9) (S9mt) (Mitochondrial small ribosoma! 396 FALSE TRUE FALSE FALSE FALSE FALSE subunit protein uS9m) 3-beta-hydroxysteroid-Deita(8),Deita(7)- isomerase (EC 5.3.3.5) (Cholestenol Deita- Q15125 EBP isomerase) (Delta(8)-Delta(7) sterol 230 TRUE TRUE TRUE TRUE TRUE TRUE isomerase) (D8-D7 sterol isomerase) (Emopamil-binding protein) 3-hydroxyacy!-CoA dehydrogenase type-2 (EC . . .35) ( 7-beta-hydroxysteroid dehydrogenase 10) (17-beta-HSD 10) (EC 1. 1 . 1 .51) (3-hydroxy-2-methylbutyryl-CoA dehydrogenase) (EC 1.1 . 1 .178) (3- 0 HSD17B1 dehydrogenase type ) Q99714 Q (Endoplasmic reticulum-associated amyloid 261 FALSE FALSE FALSE FALSE FALSE FALSE beta-peptide-binding protein) (Mitochondria! ribonuclease P protein 2) (Mitochondrial RNase P protein 2) (Short chain dehydrogenase/reductase family 5C member 1) (Short-chain type dehydrogenase/reductase XH98G2) (Type I HADH)

3-ketoacyl-CoA thiolase, mitochondrial (EC 2.3.1 .16) (Acety!-CoA acyltransferase) (Beta- P42765 ACAA2 397 FALSE FALSE FALSE TRUE FALSE FALSE ketothiolase) (Mitochondrial 3-oxoacyl-CoA -4 thiolase) (T1)

3-ketoacyl-CoA thiolase, peroxisomal (EC 2.3.1 .16) (Acetyi-CoA acyltransferase) (Beta- P091 10 ACAA1 424 TRUE FALSE FALSE FALSE TRUE FALSE ketothiolase) (Peroxisomal 3-oxoacyi-CoA thiolase) 3-mercaptopyruvate sulfurtransferase (MST) P25325 PST 297 FALSE FALSE TRUE FALSE TRUE FALSE (EC 2.8.1 .2) 3'(2'),5'~bisphosphate nucleotidase 1 (EC 095861 BPNT1 3.1 .3.7) (Bisphosphate 3'-nucieotidase 1) 308 TRUE FALSE FALSE FALSE FALSE FALSE (PAP-inositol 1,4-phosphatase) (PIP) 39S ribosomal protein L 1, mitochondrial Q9BYD6 1RPL1 (L1mt) (MRP-L1) (Mitochondrial large 325 FALSE FALSE FALSE FALSE FALSE FALSE ribosomal subunit protein uL1m)

39S ribosomal protein L10, mitochondrial (L10mt) (MRP-L10) (39S ribosomal protein L8, Q7Z7H8 1RPL10 261 FALSE FALSE FALSE FALSE FALSE FALSE mitochondrial) (L8mt) (MRP-L8) (Mitochondrial large ribosomal subunit protein uL10m) 39S ribosomal protein L39, mitochondrial (L39mt) (MRP-L39) (39S ribosornai protein L5, Q9NYK5 MRPL39 338 FALSE FALSE FALSE FALSE FALSE FALSE mitochondrial) (L5mt) (MRP-L5) (Mitochondrial Iarge ribosomal subunit protein rnL39)

39S ribosomal protein L46, mitochondrial Q9H2W6 MRPL46 (L46mt) (MRP-L46) (Mitochondrial Iarge 279 FALSE FALSE FALSE FALSE FALSE FALSE ribosomal subunit protein mL46) (P2ECSL)

4-trimethylaminobutyraldehyde dehydrogenase (TMABADH) (EC 1.2 1.47) (Aldehyde dehydrogenase E3 isozyme) (Aldehyde dehydrogenase family 9 member A1) (EC 1.2.1 .3) (Gamma- P49189 ALDH9A1 494 FALSE FALSE FALSE FALSE FALSE FALSE aminobutyraldehyde dehydrogenase) (EC 1.2. 1.19) (R-aminobutyraidehyde dehydrogenase) [Cleaved into: 4- trimethyiaminobutyraldehyde dehydrogenase, N-termina!ly processed] 40S ribosomal protein S10 (Small ribosomal P46783 RPS10 165 FALSE FALSE FALSE TRUE FALSE TRUE subunit protein eSIO) 40S ribosomal protein S 11 (Small ribosomal P62280 RPS1 1 158 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS17) 40S ribosomal protein S12 (Small ribosomal P2539S RPS12 132 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eS12) 40S ribosomal protein S13 (Small ribosomal P62277 RPS13 151 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS15) 40S ribosomal protein S14 (Small ribosomal P82263 RPS14 151 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS1 1) 40S ribosomal protein S15 (RIG protein) P62841 RPS15 145 FALSE FALSE FALSE FALSE FALSE FALSE (Small ribosomal subunit protein uS19) 40S ribosomal protein S15a (Small ribosomal P62244 RPS15A 130 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS8) 40S ribosomal protein S16 (Small ribosomal P62249 RPS16 146 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS9) 40S ribosoma! protein S17 (Smal! ribosornal P087Q8 RPS17 135 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eS17) 40S ribosoma! protein S18 (Ke-3) (Ke3) (Small P62269 RPS18 152 FALSE FALSE FALSE FALSE FALSE FALSE ribosornal subunit protein uS13) 40S ribosornal protein S19 (Smal! ribosornal P39019 RPS19 145 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eS19) 40S ribosoma! protein S2 (40S ribosornal P15880 RPS2 protein S4) (Protein LLRep3) (Small ribosoma! FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS5) 40S ribosoma! protein S20 (Small ribosornal P60866 RPS20 119 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS10) 40S ribosoma! protein S21 (Small ribosornal P63220 RPS21 83 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eS21) 40S ribosoma! protein S23 (Small ribosornal P62266 RPS23 143 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS12) 40S ribosoma! protein S24 (Small ribosornal P62847 RPS24 133 FALSE FALSE FALSE TRUE TRUE TRUE subunit protein eS24) 40S ribosoma! protein S25 (Small ribosornal P62851 RPS25 125 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eS25) 40S ribosoma! protein S26 (Small ribosornal P62854 RPS26 115 F S ! F S FA L TRUE TRUE TRUE subunit protein eS26) 40S ribosoma! protein S27 (Metailopan- P42677 RPS27 stimuiin 1) (MPS-1) (Small ribosornal subunit 84 FALSE FALSE FALSE FALSE FALSE FALSE protein eS27) 40S ribosoma! protein S28 (Small ribosornal P62857 RPS28 69 F ! FALSEi FALSE F L FALSE FALSE subunit protein eS28) 40S ribosoma! protein S3 (EC 4.2.99.18) P23396 RPS3 243 FALSE FA L E FA L FALSE FALSE (Small ribosoma! subunit protein uS3) 40S ribosoma! protein S30 (Small ribosornal P62861 FAU 59 FALSE FALSE FALSE FA L E FALSE FALSE subunit protein eS30) 40S ribosoma! protein S3a (Small ribosornal P61247 RPS3A subunit protein eS1) (v-fos transformation 264 TRUE FALSE TRUE FALSE FALSE FALSE effector protein) (Fte-1) 40S ribosomal protein S4, X isoform (SCR10) P62701 RPS4X (Single copy abundant mRNA protein) (Small 6 3 FALSE FALSE FALSE FALSE FALSE FALSE ribosomal subunit protein eS4)

40S ribosomal protein S5 (Small ribosomal P46782 RPS5 subunit protein uS7) [Cleaved into: 40S FALSE FALSE FALSE FALSE FALSE FALSE ribosomal protein S5, N-terminaily processed]

40S ribosomal protein S6 (Phosphoprotein P62753 RPS6 149 FALSE FALSE FALSE FALSE FALSE FALSE NP33) (Small ribosomal subunit protein eS6) 40S ribosomal protein S7 (Small ribosomal P62081 RPS7 194 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eS7) 40S ribosomal protein S8 (Small ribosomal P62241 RPS8 2 8 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eS8) 40S ribosomal protein S9 (Small ribosomal 194 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uS4)

40S ribosomal protein SA (37 kDa iaminin receptor precursor) (37LRP) (37/67 kDa Iaminin receptor) (LRP/LR) (67 kDa Iaminin receptor) (67LR) (Colon carcinoma iaminin- P08865 RPSA binding protein) (Laminin receptor 1) (LarnR) 295 FALSE FALSE FALSE FALSE FALSE FALSE (Laminin-binding protein precursor p40) (LBP/p40) (Multidrug resistance-associated protein MGr1-Ag) (NEM/1CHD4) (Small ribosomal subunit protein uS2)

4F2 cell-surface antigen heavy chain (4F2hc) (4F2 heavy chain antigen) (Lymphocyte P08195 SLC3A2 630 TRUE TRUE FALSE FALSE FALSE FALSE activation antigen 4F2 large subunit) (Solute carrier family 3 member 2) (CD antigen CD98)

5'-3' exoribonuciease 2 (EC 3 1.13.-) (DHM1- Q9H0D6 XRN2 950 FALSE FALSE FALSE FALSE FALSE FALSE ike protein) (DHP protein) 5'-AMP-activated protein kinase catalytic subunit alpha- (A PK subunit a!pha-1) (EC 2 7. 1.1) (Acetyl-CoA carboxylase kinase) Q13131 PRKAA1 (ACACA kinase) (EC 2.7.1 1.27) 559 FALSE FALSE FALSE FALSE FALSE FALSE (Hyclroxymethylgiutaryl-CoA reductase kinase) (H GC R kinase) (EC 2.7.1 1.31) (Tau-protein kinase PRKAA1) (EC 2.7.1 1.26)

5'-AMP-activated protein kinase subunit P54619 PRKAG1 gamma-1 (A PK gammal) (A PK subunit 331 FALSE FALSE FALSE FALSE FALSE TRUE gamma-1) (AMPKg) 5'-nucieotidase domain-containing protein 1 Q5TFE4 NT5DC1 455 FALSE FALSE FALSE FALSE FALSE FALSE (EC 3.1 .3.-) 55 kDa erythrocyte membrane protein (p55) Q00013 1PP1 466 FALSE FALSE FALSE FALSE FALSE FALSE (Membrane protein, paimitoyiated 1) 6-pbospbog!uconate dehydrogenase, P52209 PGD 483 FALSE FALSE! FALSE FALSE FA LS decarboxylating (EC 1. 1 . 1 .44) 6-phosphogluconoiactonase (6PGL) (EC -4 095336 PGLS 258 FALSE F LS E FALSE! FALSE FALSE FALSE 3.1 . 1 .31)

60 kDa heat shock protein, mitochondrial (EC 3.6.4.9) (60 kDa chaperonin) (Chaperonin 60) P10809 HSPD1 (CPN60) (Heat shock protein 60) (HSP-60) 573 FALSE FALSE A LSE FALSE FALSE FALSE (Hsp60) (HuCHA60) (Mitochondrial matrix protein P1) (P60 lymphocyte protein)

60 kDa SS-A/Ro ribonucleoprotein (60 kDa Ro protein) (60 kDa ribonucleoprotein Ro) (RoRNP) (Ro 60 kDa autoantigen) (Sjoegren P10155 TROVE2 538 FALSE FALSE FALSE FALSE FALSE FALSE syndrome antigen A2) (Sjoegren syndrome type A antigen) (SS-A) (TROVE domain family member 2) 60S acidic ribosomai protein P0 (60S P05388 ribosomal protein L10E) (Large ribosomai 317 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL10) 60S acidic ribosomai protein P 1 (Large P05386 114 FALSE FALSE FALSE FALSE FALSE FALSE ribosomai subunit protein P1) 60S acidic ribosomal protein P2 (Large P05387 RPLP2 ribosomal subunit protein P2) (Renal 115 FALSE FALSE FALSE FALSE FALSE FALSE carcinoma antigen NY-REN-44) 60S ribosomal protein L10 (Laminin receptor P27635 RPL10 homolog) (Large ribosomal subunit protein 214 FALSE FALSE FALSE FALSE FALSE FALSE uL16) (Protein QM) (Tumor suppressor QM)

60S ribosomal protein L10a (CSA-19) (Large ribosomal subunit protein uL1) (Neural P629Q6 RPL10A 217 FALSE FALSE FALSE FALSE FALSE FALSE precursor cell expressed developmentally down-regulated protein 6) (NEDD-6)

60S ribosomal protein L (CLL-associated P62913 RPL1 antigen K - 2) (Large ribosomal subunit 178 FALSE FALSE FALSE FALSE FALSE FALSE protein uL5) 60S ribosomal protein L 2 (Large ribosomal P30050 RPL12 165 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL1 1)

-4 60S ribosomal protein L13 (Breast basic -4 P26373 RPL13 conserved protein 1) (Large ribosomal subunit 2 11 FALSE FALSE FALSE FALSE FALSE FALSE protein eL13) 60S ribosomal protein L13a (23 kDa highly P40429 RPL13A basic protein) (Large ribosomal subunit protein 203 FALSE FALSE FALSE FALSE FALSE FALSE uL13) 60S ribosomal protein L14 (CAG-ISL 7) (Large P50914 RPL14 .15 FALSE FALSE FALSE FALSE FALSE FALSE ribosomal subunit protein eL14) 60S ribosomal protein L15 (Large ribosomal P61313 RPL15 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL15) 60S ribosomal protein L17 (60S ribosomal P18621 RPL17 protein L23) (Large ribosomal subunit protein 184 FALSE FALSE FALSE FALSE FALSE FALSE uL22) (PD-1) 60S ribosomal protein L18 (Large ribosomal QQ7020 RPL18 188 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL18) 60S ribosomal protein L18a (Large ribosomal QQ2543 RPL18A 176 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL20) 60S ribosomal protein L19 (Large ribosomal RPL19 196 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL19) 60S ribosoma! proiein L21 (Large ribosomal P46778 RPL21 160 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL21) 60S ribosoma! protein L22 (EBER-associated protein) (EAP) (Epstein-Barr virus small RNA- P35268 RPL22 associated protein) (Heparin-binding protein 128 FALSE FALSE FALSE FALSE FALSE FALSE HBp15) (Large ribosomal subunit protein eL22) 60S ribosomal protein L23 (60S ribosomal P62829 RPL23 protein L17) (Large ribosomal subunit protein 140 FALSE FALSE FALSE FALSE FALSE FALSE uL14) 60S ribosomal protein L23a (Large ribosomal P62750 RPL23A 156 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL23) 60S ribosomal protein L24 (60S ribosomal P83731 RPL24 protein L30) (Large ribosomal subunit protein 157 FALSE FALSE FALSE FALSE FALSE FALSE eL24) 60S ribosomal protein L26 (Large ribosomal P61254 RPL26 145 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL24) 60S ribosomal protein L27 (Large ribosomal -4 P61353 RPL27 136 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL27) 60S ribosomal protein L27a (Large ribosomal P46776 RPL27A 148 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL15) 60S ribosomal protein L28 (Large ribosomal P46779 RPL28 137 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL28) 60S ribosomal protein L29 (Ceil surface P47914 RPL29 heparin-binding protein HIP) (Large ribosomal 159 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL29) 60S ribosomal protein L3 (HIV-1 TAR RNA- P39023 RPL3 binding protein B) (TARBP-B) (Large 403 FALSE FALSE FALSE FALSE FALSE FALSE ribosomal subunit protein uL3) 60S ribosomal protein L30 (Large ribosomal P62888 RPL30 , . subunit protein eL30) 60S ribosomal protein L31 (Large ribosomal P62899 RPL31 125 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL31) 60S ribosomal protein L32 (Large ribosomal P62910 RPL32 135 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL32) 60S ribosomai protein L34 (Large ribosomai P49207 RPL34 117 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL34) 60S ribosomai protein L35 (Large ribosomai P42766 RPL35 123 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL29) 60S ribosomai protein L35a (Ceil growth- P 077 RPL35A inhibiting gene 33 protein) (Large ribosomai 110 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL33) 60S ribosomai protein L36 (Large ribosomai Q9Y3U8 RPL36 105 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL36) 60S ribosomai protein L36a (60S ribosomai protein L44) (Ceil growth-inhibiting gene 15 P83881 RPL36A protein) (Ceil migration-inducing gene 6 106 FALSE FALSE FALSE FALSE FALSE FALSE protein) (Large ribosomai subunit protein eL42) ' 60S ribosomai protein L36a-like (Large Q969Q0 RPL36AL 1 6 FALSE FALSE FALSE FALSE FALSE FALSE ribosomai subunit protein eL42-like) 60S ribosomai protein L37 (G1 .16) (Large P81927 RPL37 97 FALSE FALSE FALSE FALSE FALSE FALSE ribosomai subunit protein eL37) 60S ribosomai protein L37a (Large ribosomai P61513 R.PL37A 92 FALSE FALSE FALSE TRUE TRUE TRUE subunit protein eL43) 60S ribosomai protein L38 (Large ribosomai P63173 RPL38 70 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL38) 60S ribosomai protein L39 (Large ribosomai P62891 RPL39 5 1 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein eL39) 60S ribosomai protein L4 (60S ribosomai P36578 RPL4 protein L1) (Large ribosomai subunit protein 427 FALSE FALSE FALSE FALSE FALSE FALSE uL4) 60S ribosomai protein L5 (Large ribosomai P46777 RPL5 297 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL18)

60S ribosomai protein L6 (Large ribosomai subunit protein eL6) (Neoplasm-related protein Q02878 RPL6 288 FALSE FALSE FALSE FALSE FALSE FALSE C140) (Tax-responsive enhancer element- binding protein 107) (TaxREB107)

60S ribosomai protein L7 (Large ribosomai P18124 RPL7 248 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL30) 60S ribosomal protein L7a (Large ribosomal P62424 RPL7A subunit protein eL8) (PLA-X polypeptide) 266 FALSE FALSE FALSE FALSE FALSE FALSE (Surfeit locus protein 3) 60S ribosomal protein L8 (Large ribosomal P62917 RPL8 257 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL2) 60S ribosomal protein L9 (Large ribosomal P32969 RPL9 192 FALSE FALSE FALSE FALSE FALSE FALSE subunit protein uL6)

7-debydrocholesterol reductase (7-DHC Q9UB 7 DHCR7 reductase) (EC 1.3.1 .21) (Putative sterol 475 FALSE FALSE FALSE FALSE FALSE FALSE reductase SR-2) (Sterol Delta(7)-reductase) 78 kDa glucose-regulated protein (GRP-78) (Endoplasmic reticulum lumenal Ca(2+)- P 1 1021 HSPA5 binding protein grp78) (Heat shock 70 kDa 654 FALSE FALSE FALSE FALSE FALSE FALSE protein 5) (Immunoglobulin heavy chain- binding protein) (BiP)

7SK snRNA methylphosphate capping Q7L2J0 EPCE enzyme (MePCE) (EC 2.1 .1.-) (Bicoid- 689 FALSE FALSE FALSE FALSE FALSE FALSE interacting protein 3 homolog) (Bin3 homolog)

A-kinase anchor protein 1, mitochondrial (A- kinase anchor protein 149 kDa) (AKAP 149) (Dual specificity A-kinase-anchoring protein 1) Q92667 AKAP1 903 FALSE FALSE FALSE FALSE FALSE FALSE (D-AKAP-1) (Protein kinase A-anchoring protein 1) (PRKA1) (Spermatid A-kinase anchor protein 84) (S-AKAP84) A-kinase anchor protein 8 (AKAP-8) (A-kinase 043823 AKAP8 692 FALSE FALSE FALSE FALSE FALSE FALSE anchor protein 95 kDa) (AKAP 95) Acetolactate synthase-like protein (EC 2.2.1 .-) A 1L0T0 LVBL 632 FALSE FALSE FALSE FALSE TRUE FALSE (ilvB-iike protein)

Acetyl-CoA acetyltransferase, cytosolic (EC Q9BWD1 ACAT2 2.3.1 .9) (Acetyl-CoA transferase-like protein) 397 FALSE FALSE FALSE TRUE TRUE TRUE (Cytosolic acetoacetyl-CoA thioiase) Acetyl-CoA aceiyitransferase, mitochondrial P24752 ACAT1 427 FALSE FALSE FALSE FALSE FALSE FALSE (EC 2.3 1.9) (Acetoacety!-CoA thiolase) (T2) Acetyi-CoA carboxylase 1 (ACC1) (EC Q13085 ACACA 6.4.1 .2) (ACC-alpha) [Includes: Biotin 2346 FALSE FALSE FALSE FALSE FALSE FALSE carboxylase (EC 6.3.4.14)]

Acidic leucine-rich nuclear phosphoprotein 32 family member A (Acidic nuclear phosphoprotein pp32) (pp32) (Leucine-rich ANP32A acidic nuclear protein) (LANP) (Mapmodulin) 249 FALSE FALSE FALSE FALSE FALSE FALSE (Potent heat-stable protein phosphatase 2A inhibitor 1 PP2A) (Putative HLA-DR- associated protein i) (PHAPi)

Acidic leucine-rich nuclear phosphoprotein 32 family member B (Acidic protein rich in Q92688 ANP32B 251 FALSE FALSE FALSE TRUE FALSE TRUE leucines) (Putative HLA-DR-associated protein I-2) (PHAPI2) (Siiver-stainable protein SSP29)

Acidic leucine-rich nuclear phosphoprotein 32 Q9BTT0 E family member E (LANP-like protein) (LANP- 268 TRUE FALSE FALSE TRUE TRUE TRUE L) Aconitate hydratase, mitochondrial (Aconitase) Q99798 AC02 780 FALSE FALSE FALSE FALSE FALSE FALSE (EC 4.2.1 .3) (Citrate hydro-iyase)

Actin-like protein 6A (53 kDa BRG1- associated factor A) (Actin-related protein 096019 ACTL6A 429 FALSE FALSE FALSE FALSE FALSE FALSE Baf53a) (ArpNbeta) (BRG1 -associated factor 53A) (BAF53A) (INO80 complex subunit K)

P61 160 Actin-related protein 2 (Actin-like protein 2) 394 FALSE FALSE! FALSE! FALSE FALSE FALSE Actin-related protein 2/3 complex subunit 1B 015143 ARPC1 B 3 FALSE! FALSEi FALSE FALSE FALSE FALSE (Arp2/3 complex 4 1 kDa subunit) (p41-ARC) Actin-related protein 2/3 complex subunit 3 015145 ARPC3 178 FALSE FALSE FALSE FALSE FALSE FALSE (Arp2/3 complex 2 1 kDa subunit) (p21-ARC)

Actin-related protein 2/3 complex subunit 4 P59998 ARPC4 168 TRUE FALSE FALSE FALSE FALSE FALSE (Arp2/3 complex 20 kDa subunit) (p20-ARC)

P61 158 ACTR3 Actin-related protein 3 (Actin-iike protein 3) 418 TRUE FALSE FALSE FALSE FALSE FALSE Actin, alpha cardiac muscle 1 (Alpha-cardiac P68032 ACTC1 377 FALSE FALSE FALSE FALSE FALSE FALSE actin)

Actin, cytoplasmic 1 (Beta-actin) [Cleaved into: P607Q9 ACTB 375 FALSE FALSE FALSE FALSE FALSE FALSE Actin, cytoplasmic 1, N-terminaily processed] Activated RNA polymerase transcriptional P53999 SUB1 coactivator p15 (Positive cofactor 4) (PC4) 127 FALSE FALSE FALSE FALSE FALSE FALSE (SUB1 homoiog) (p14) Activating signal cointegrator 1 complex Q9H1 8 ASCC2 subunit 2 (ASC-1 complex subunit p100) 757 FALSE FALSE FALSE FALSE FALSE FALSE (Trip4 complex subunit p100) Activating signal cointegrator 1 complex subunit 3 (EC 3.6.4 12) (ASC-1 complex Q8N3C0 ASCC3 2202 FALSE FALSE FALSE FALSE FALSE FALSE subunit p200) (ASC1p200) (Helicase, ATP binding 1) (Trip4 complex subunit p200) Activator of 90 kDa heat shock protein 095433 AHSA1 338 FALSE FALSE FALSE FALSE FALSE FALSE ATPase homoiog 1 (AHA1) (p38) Acyl-CoA dehydrogenase family member 9 , Q9H845 ACAD9 321 FALSE FALSE FALSE TRUE TRUE TRUE mitochondrial (ACAD-9) (EC 1.3.99.-) Acyl-CoA desaturase (EC 1.14.19.1) (Delta(9)- desaturase) (Delta-9 desaturase) (Fatty acid OQ0767 SCD 359 FALSE FALSE FALSE FALSE FALSE FALSE desaturase) (Stearoyl-CoA desaturase) (hSCD1) Acyl-profein thioesterase 1 (APT-1) (hAPT1) 075608 LYPLA1 (EC 3.1 .2.-) (Lysophosphoiipase 1) 230 FALSE TRUE TRUE FALSE FALSE FALSE (Lysophosphoiipase ) (LPL-i) (LysoPLA ) Acyl-proiein thioesterase 2 (APT-2) (EC 3.1 .2.- 095372 2 231 FALSE FALSE FALSE FALSE FALSE FALSE ) (Lysophospho!ipase I) (LPL-II) (LysoPLA II)

Acylamino-acid-releasing enzyme (AARE) (EC 3.4.19.1) (Acy!-peptide hydrolase) (APH) P13798 APEH 732 FALSE FALSE FALSE FALSE FALSE FALSE (Acylaminoacyl-peptidase) (Oxidized protein hydrolase) (OPH) Acylglycerol kinase, mitochondrial (hAGK) (EC 2.7.1 .107) (EC 2.7.1 .94) (Multiple substrate Q53H12 AGK 422 TRUE TRUE FALSE TRUE TRUE F L i lipid kinase) (HsMuLK) (MuLK) (Multi- substrate lipid kinase) Adaptin ear-binding coat-associated protein 2 NECAP2 (NECAP endocytosis-associated protein 2) 263 TRUE FALSE FALSE FALSE F FALSE (NECAP-2) Adenine phosphoribosyltransferase (APRT) P07741 APRT 180 FALSE FALSE FALSE FA S . FALSE FALSE (EC 2.4.2.7) Adenosylhomocysteinase 3 (AdoHcyase 3) (EC 3.3.1 .1) (IP(3)Rs binding protein released with iP(3) 2) (IRBIT2) (Long-IRBIT) (S- Q96HN2 AHCYL2 6 11 FALSE FALSE FALSE F . FALSE FALSE adenosyl-L-homocysteine hydrolase 3) (S- adenosylhomocysteine hydro ase- ke protein 2) Adenosylhomocysteinase (AdoHcyase) (EC P23526 AHCY 3.3.1 .1) (S-adenosyl-L-homocysteine 432 FALSE FALSE FALSE FALSE FALSE FALSE hydrolase)

Adenylate kinase 2 , mitochondrial (AK 2) (EC 2.7.4.3) (ATP-A P transphosphorylase 2) (ATP:AMP phosphotransferase) (Adenylate P54819 AK2 239 FALSE FALSE FALSE FALSE FALSE FALSE monophosphate kinase) [Cleaved into: Adenylate kinase 2 , mitochondrial, N- terminally processed]

Adenylosuccinate lyase (ADSL) (ASL) (EC P30566 484 FALSE FALSE FALSE FALSE FALSE FALSE 4.3.2.2) (Adenylosuccinase) (ASase) Adenylosuccinate synthetase isozyme 2 (AMPSase 2) (AdSS 2) (EC 6.3.4.4) (Adenylosuccinate synthetase, acidic isozyme) P30520 ADSS 456 FALSE FALSE FALSE FALSE FALSE FALSE (Adenylosuccinate synthetase, liver isozyme) (L-type adenylosuccinate synthetase) (IMP-- aspartate ligase 2)

Q01518 CAP1 Adenylyl cyclase-associaied protein 1 (CAP 1) 475 FALSE FALSE FALSE FALSE FALSE FALSE

P612Q4 ARF3 ADP-ribosylation factor 3 181 FALSE FALSE FALSE FALSE FALSE FALSE P18085 ARF4 ADP-ribosylation factor 4 180 FALSE FALSE FALSE FALSE FALSE FALSE P84085 ARF5 ADP-ribosylation factor 5 180 FALSE FALSE FALSE FALSE FALSE FALSE P62330 ARF6 ADP-ribosylation factor 6 175 FALSE FALSE FALSE FALSE FALSE FALSE ADP- bosy a i r factor GTPase-activating protein 1 (ARF GAP 1) (ADP-ribosylation ARFGAP Q8N6T3 factor 1 GTPase-activating protein) (ARF1 406 FALSE TRUE FALSE FALSE FALSE FALSE 1 GAP) (ARF1 -directed GTPase-activating protein) P40616 ARL1 ADP-ribosylation factor-like protein 1 181 FALSE FALSE FALSE FALSE FALSE ADP-ribosylation factor-like protein 6- interacting protein 1 (ARL-6-interacting protein Q15041 ARL6IP1 203 TRUE FALSE FALSE FALSE FALSE 1) (Aip-1) (Apoptotic regulator in the membrane of the endoplasmic reticulum) ADP-ribosylation factor-like protein 6- interacting protein 4 (ARL-6-interacting protein Q66PJ3 ARL6IP4 4) (Aip-4) (HSP-975) (HSVI-binding protein) 421 FALSE FALSE FALSE FALSE FALSE FALSE (SR-15) (SRp25) (SR-25) (Splicing factor SRrp37) ADP-sugar pyrophosphatase (EC 3.6.1 .13) (8- oxo-dGDP phosphatase) (EC 3.6 1.58) (Nuclear ATP-synthesis protein NUDIX5) (EC Q9UKK9 NUDT5 219 FALSE FALSE FALSE FALSE FALSE FALSE 2.7.7.96) (Nucleoside diphosphate-iinked moiety X motif 5) (Nudix motif 5) (hNUDT5) (YSA1 H) ADP/ATP translocase 2 (ADP.ATP carrier proiein 2) (ADP.ATP carrier protein, fibroblast isoform) (Adenine nucleotide iranslocator 2) P05141 SLC25A5 TRUE TRUE FALSE TRUE FALSE TRUE (ANT 2) (Solute carrier family 25 member 5} [Cleaved into: ADP/ATP translocase 2 , N- terminaliy processed]

ADP/ATP translocase 3 (ADP.ATP carrier proiein 3) (ADP.ATP carrier protein, isoform T2) (ANT 2) (Adenine nucleotide translocator P12236 SLC25A6 298 FALSE FALSE FALSE FALSE FALSE FALSE 3) (ANT 3) (Solute carrier family 25 member 6) [Cleaved into: ADP/ATP translocase 3 , N- terminaliy processed] AFG3-iike protein 2 (EC 3.4.24.-) (Paraplegin- Q9Y4W6 AFG3L2 797 TRUE TRUE FALSE FALSE FALSE FALSE ike proiein)

Afiatoxin B 1 aldehyde reductase member 2 (EC 1. 1 . 1 .n1 1) (AFB1 aldehyde reductase 1) 043488 AKR7A2 359 F L3 Ε A Ξ F L F Ε FA Ξ FA L EE (AFB1-AR 1) (Aldoketoreductase 7) (Succinic semialdehyde reductase) (SSA reductase)

AH receptor-interacting protein (AIP) (Aryl- hydrocarbon receptor-interacting protein) 000170 A P 330 TRUE FALSE FA FA i FALSE FALSE (HBV X-associated protein 2) (XAP-2) (Immunophilin homolog ARA9) Q9NRG9 AAAS Aladin (Adracalin) 546 TRUE TRUE TRUE FALSE TRUE FALSE Alanine-tRNA ligase, cytoplasmic (EC P49588 AARS 6.1 . 1 .7) (Alanyl-tRNA synthetase) (AlaRS) 968 FALSE FALSE FALSE FALSE FALSE FALSE (Renal carcinoma antigen NY-REN-42) Alanine-tRNA ligase, mitochondrial (EC Q5JTZ9 AARS2 985 FALSE FALSE FALSE FALSE FALSE FALSE 6.1 . 1 .7) (Alanyl-tRNA synthetase) (AlaRS) Alanyl-tRNA editing protein Aarsdl (Alanyl- Q9BTE6 AARSD1 412 FALSE FALSE FALSE FALSE TRUE FALSE tRNA synthetase domain-containing protein Alcohol dehydrogenase [NADP(+)] (EC P14550 AKR1A1 1. 1 . 1 2) (Aldehyde reductase) (Aldo-keto 325 FALSE FALSE FALSE FALSE FALSE FALSE reductase family 1 member A1)

Alcohol dehydrogenase class-3 (EC 1. 1 . 1 .1) (Alcohol dehydrogenase 5) (Alcohol dehydrogenase class chi chain) (Alcohol dehydrogenase class-Ill) (Glutathione- P 1766 ADH5 374 FALSE FALSE FALSE FALSE FALSE FALSE dependent formaldehyde dehydrogenase) (FALDH) (FDH) (GSH-FDH) (EC 1.1 . 1 .-) (S- (hydroxymethyl)glutathione dehydrogenase) (EC 1. 1 . 1 .284) '

Alkyldihydroxyacetonephosphate synthase, peroxisomal (Alkyl-DHAP synthase) (EC OQ01 16 AGPS 658 FALSE FALSE FALSE FALSE FALSE FALSE 2.5.1 .26) (Aging-associated gene 5 protein) (Alkyiglycerone-phosphate synthase)

Alpha-actinin-1 (Alpha-actinin cytoskeietai P12814 ACTN1 isoform) (F-actin cross-linking protein) (Non- 892 FALSE FALSE FALSE FALSE FALSE FALSE muscle aipha-actinin-l)

043707 ACTN4 Alpha-actinin-4 (Non-muscle alpha-actinin 4) 9 11 FALSE FALSE FALSE FALSE FALSE FALSE

Alpha-centractin (Centractin) (ARP1) (Actin- P61 163 ACTR1A 376 FALSE FALSE FALSE FALSE FALSE FALSE RPV) (Centrosome-associated actin homoiog)

Alpha-enoiase (EC 4.2.1.1 1) (2-phospho-D- glycerate hydro-lyase) (C-myc promoter- binding protein) (Enolase 1) (MBP-1) (MPB-1) P06733 EN01 434 FALSE FALSE FALSE FALSE FALSE FALSE (Non-neural enolase) (NNE) (Phosphopyruvate hydratase) (Plasminogen- binding protein) Alpha-soluble NSF attachment protein (SNAP- P54920 NAPA alpha) (N-ethylmaleimide-sensitive factor 295 TRUE TRUE FALSE TRUE TRUE TRUE attachment protein alpha) P40222 TXLNA Alpha-taxilin 546 TRUE FALSE FALSE TRUE FALSE FALSE Amidophosphoribosyltransferase (ATase) (EC 2.4.2 14) (Giutamine Q06203 PPAT 517 FALSE FALSE FALSE FALSE FALSE FALSE phosphoribosylpyrophosphate amidotransf erase) (GPAT) Aminoacyi tRNA synthase complex-interacting multifunctional protein 1 (Multisynthase complex auxiliary component p43) [Cleaved into: Endothelial monocyte-activating AIMP1 312 FALSE FALSE FALSE FALSE TRUE FALSE polypeptide 2 (EMAP-2) (Endothelial monocyte-activating polypeptide ) (EMAP-II) (Small inducible cytokine subfamily E member 1)] Aminoacyi tRNA synthase complex-interacting multifunctional protein 2 (Multisynthase Q13155 AI P2 320 FALSE FALSE FALSE TRUE FALSE TRUE complex auxiliary component p38) (Protein JTV-1) Aminopeptidase B (AP-B) (EC 3.4.1 1.6) Q9H4A4 RNPEP (Arginine aminopeptidase) (Arginyi 650 FALSE FALSE FALSE FALSE FALSE FALSE -4 aminopeptidase) Anamorsin (Cytokine-induced apoptosis Q6FI81 CIAPIN1 inhibitor 1) (Fe-S cluster assembly protein 312 FALSE FALSE FALSE FALSE FALSE FALSE DRE2 homoiog) Anaphase-promoting complex subunit 7 Q9UJX3 ANAPC7 599 FALSE FALSE FALSE TRUE FALSE TRUE (APC7) (Cyclosome subunit 7)

Annexin A 1 (Annexin ) (Annexin-1) (Caipactin P04083 ANXA1 II) (Calpactin-2) (Chromobindin-9) (Lipocortin 346 FALSE FALSE FALSE FALSE FALSE FALSE ) (Phosphoiipase A2 inhibitory protein) (p35)

Annexin A 1 (56 kDa autoantigen) (Annexin P50995 ANXA1 X ) (Annexin-1 1) (Calcyclin-associated 505 FALSE FALSE FALSE FALSE FALSE FALSE annexin 50) (CAP-50) Annexin A2 (Annexin II) (Annexin-2) (Caipactin heavy chain) (Caipactin- 1 heavy P07355 ANXA2 chain) (Chromobindin-8) (Lipocortin II) 339 FALSE FALSE FALSE FALSE FALSE FALSE (Placental anticoagulant protein IV) (PAP-IV) (Protein ) (p36) Annexin A5 (Anchorin C ) (Annexin V) (Annexin-5) (Calphobindin ) (CBP-I) (Endonexin ) (Lipocortin V) (Placental P08758 ANXA5 anticoagulant protein 4} (PP4) (Placental 320 FALSE FALSE FALSE FALSE FALSE FALSE anticoagulant protein ) (PAP-I) (Thromboplastin inhibitor) (Vascular anticoagulant-alpha) (VAC-alpha) Annexin A7 (Annexin VI ) (Annexin-7) P20073 ANXA7 488 FALSE FALSE FALSE TRUE FALSE FALSE (Synexin) Proliferation marker protein Ki-67 (Antigen P46013 KI67 identified by monoclonal antibody Ki-67) 3256 FALSE FALSE FALSE FALSE FALSE FALSE (Antigen KI-67) (Antigen KI67) AP-1 complex subunit gamma-1 (Adaptor protein complex AP-1 subunit gamma-1) (Adaptor-related protein complex 1 subunit 043747 AP1G1 gamma-1) (Clathrin assembly protein complex 822 FALSE FALSE FALSE FALSE 1 gamma-1 large chain) (Gammal-adaptin) (Golgi adaptor HA1/AP1 adaptin subunit gamma-1)

AP-1 complex subunit mu-1 (AP-mu chain family member mu1A) (Adaptor protein complex AP-1 subunit mu-1) (Adaptor-related protein complex 1 subunit mu-1) (Clathrin Q9BXS5 AP1M1 assembly protein complex 1 mu-1 medium 423 FALSE FALSE FALSE TRUE FALSE TRUE chain 1) (Clathrin coat assembly protein AP47) (Clathrin coat-associated protein AP47) (Golgi adaptor HA1/AP1 adaptin mu-1 subunit) (Mu- adaptin 1) (Mu1A-adaptin) AP-1 complex subunit sigma-1A (Adaptor protein complex AP-1 subunit sigma-1A) (Adaptor-related protein complex 1 subunit sigma-1A) (Clathrin assembly protein complex 1 sigma-1A small chain) (Clathrin coat P61966 AP1S1 158 FALSE FALSE FALSE FALSE FALSE FALSE assembly protein AP19) (Golgi adaptor HA1/AP1 adaptin sigma-1A subunit) (HA1 19 kDa subunit) (Sigma 1a subunit of AP-1 clathrin) (Sigma-adaptin 1A) (SigmalA- adaptin) AP-2 complex subunit alpha- 1 (100 kDa coated vesicle protein A) (Adaptor protein complex AP-2 subunit alpha-1) (Adaptor- related protein complex 2 subunit alpha-1) 095782 AP2A1 977 FALSE FALSE FALSE FALSE FALSE FALSE (Alpha-adaptin A) (Alphal -adaptin) (Clathrin assembly protein complex 2 alpha-A large chain) (Plasma membrane adaptor HA2/AP2 oe adaptin alpha A subunit) AP-2 complex subunit beta (AP105B) (Adaptor protein complex AP-2 subunit beta) (Adaptor- related protein complex 2 subunit beta) (Beta- P83010 AP2B1 2-adaptin) (Beta-adaptin) (Clathrin assembly 937 FALSE FALSE FALSE TRUE TRUE TRUE protein complex 2 beta large chain) (Plasma membrane adaptor HA2/AP2 adaptin beta subunit)

AP-2 complex subunit u (AP-2 mu chain) (Adaptin-mu2) (Adaptor protein complex AP-2 subunit mu) (Adaptor-related protein complex 2 subunit mu) (Clathrin assembly protein Q96CW1 AP2M1 complex 2 mu medium chain) (Clathrin coat 435 FALSE FALSE FALSE FALSE FALSE TRUE assembly protein AP50) (Clathrin coat- associated protein AP50) (HA2 50 kDa subunit) (Plasma membrane adaptor AP-2 50 kDa protein) AP-3 complex subunit delta~1 (AP~3 complex 014617 AP3D1 subunit delta) (Adaptor-related protein 1153 FALSE FALSE FALSE FALSE FALSE FALSE complex 3 subunit delia-1) (Delta-adaptin)

Apoptosis inhibitor 5 (API-5) (Antiapoptosis done protein) (AAC-1 1) (Cell migration- Q9BZZ5 APIS inducing gene 8 protein) (Fibroblast growth 524 TRUE TRUE TRUE TRUE TRUE FALSE factor 2-interacting factor) (FIF) (Protein XAGL)

Apoptosis-inducing factor 1, mitochondrial (EC 095831 AIFM1 613 FALSE FALSE FALSE FALSE FALSE FALSE 1. 1 . 1 .-) (Programmed cell death protein 8)

Apopiotic chromatin condensation inducer in Q9UKV3 ACIN1 1341 FALSE FALSE! FALSE FALSE FALSE the nucleus (Acinus) Q9NWB6 ARGLU1 Arginine and glutamate-rich proiein 1 273 FALSE FALSE FALSE FALSE FALSE FALSE

Arginine-tRNA ligase, cytoplasmic (EC P54136 RARS 660 FALSE FALSE FALSE FALSE FALSE FALSE 6.1 . 1 .19) (Arginyl-tRNA synthetase) (ArgRS) o Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 434 FALSE FALSE FALSE FALSE FALSE FALSE Asparagine synthetase [glutamine- hydroiyzing] (EC 6.3.5.4) (Ceil cycle control P08243 ASNS 561 FALSE FALSE FALSE FALSE FALSE FALSE protein TS1 1) (Glutamine-dependent asparagine synthetase) Asparagine-tRNA ligase, cytoplasmic (EC 043776 NARS 6.1 . 1 .22) (Asparaginyl-tRNA synthetase) 548 FALSE FALSE FALSE FALSE FALSE FALSE (AsnRS) Aspartate aminotransferase, cytoplasmic (cAspAT) (EC 2.6 1.1) (EC 2 6.1.3) (Cysteine aminotransferase, cytoplasmic) (Cysteine P17174 GOT1 413 FALSE FALSE FALSE FALSE FALSE FALSE transaminase, cytoplasmic) (cCAT) (Glutamate oxaloacetate transaminase 1) (Transaminase A) Aspartate aminotransferase, mitochondrial (mAspAT) (EC 2.6.1 .1) EC 2.6.1 .7) (Fatty acid-binding protein) (FABP-1) (Glutarnate oxaloacetate transaminase 2) (Kynurenine aminotransferase 4) (Kynurenine P00505 GOT2 430 FALSE FALSE FALSE FALSE FALSE FALSE aminotransferase IV) (Kynurenine- oxogiutarate transaminase 4) (Kynurenine- oxogiutarate transaminase V) (Plasma membrane-associated fatty acid-binding protein) (FABPpm) (Transaminase A)

Aspartate-tRNA ligase, cytoplasmic (EC P14868 DARS 6.1 . 1 .12) (Aspartyl-tRNA synthetase) (AspRS) 501 FALSE FALSE FALSE FALSE FALSE FALSE (Ce l proliferation-inducing gene 40 protein)

Aspartate-tRNA ligase, mitochondrial (EC Q6PI48 DARS2 645 FALSE FALSE FALSE FALSE FALSE FALSE 6.1 . 1 .12) (Aspartyl-tRNA synthetase) (AspRS) Aspartyl/asparaginyl beta-hydroxylase (EC 1.14.1 1.16) (Aspartate beta-hydroxylase) Q12797 ASPH 758 FALSE FALSE FALSE FALSE FALSE FALSE (ASP beta-hydroxylase) (Peptide-aspartate beta-dioxygenase) Ataxin-10 (Brain protein E46 homolog) Q9UBB4 ATXN10 475 TRUE TRUE TRUE FALSE FALSE FALSE (Spinocerebellar ataxia type 10 protein) Ataxin-2-like protein (Ataxin-2 domain protein) Q8WWM1 ATXN2L 1075 FALSE FALSE FALSE FA S . FALSE FALSE (Ataxin-2-related protein) Q6DD88 ATL3 Atlastin-3 (EC 3.6.5.-) 541 FALSE TRUE FALSE TRUE TRUE FALSE ATP synthase F(0) complex subunit B 1, mitochondrial (ATP synthase proton- P24539 ATP5F1 transporting mitochondrial F(0) complex 256 TRUE TRUE FALSE TRUE TRUE TRUE subunit B1) (ATP synthase subunit b) (ATPase subunit b) T ATP6 ATP synthase subunit a (F-ATPase prote 226 TRUE TRUE TRUE FALSE FALSE FALSE

P25705 ATP5A1 ATP synthase subunit alpha, mitochondrial 553 FALSE FALSE FALSE FALSE FALSE FALSE ATP synthase subunit beta, mitochondrial (EC P06576 ATP5B 529 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.3 14) ATP synthase subunit d , mitochondrial 075947 ATP5H 161 FALSE FALSE FALSE FALSE FALSE FALSE (ATPase subunit d) ATP synthase subunit epsilon, mitochondrial P56381 ATP5E 5 1 FALSE FALSE FALSE FALSE FALSE FALSE (ATPase subunit epsilon) P56134 ATP5J2 ATP synthase subunit f, mitochondrial 94 TRUE TRUE FALSE FALSE FALSE FALSE ATP synthase subunit g , mitochondrial 075964 ATP5L 103 FALSE TRUE FALSE FALSE FALSE FALSE (ATPase subunit g) ATP synthase subunit gamma, mitochondrial P36542 ATP5C1 298 FALSE FALSE FALSE FALSE FALSE FALSE (F-ATPase gamma subunit) ATP synthase subunit O, mitochondrial ATP50 (Oligomycin sensitivity conferral protein) 213 FALSE FALSE FALSE FALSE FALSE FALSE (OSCP) ATP-binding cassette sub-family B member 10, mitochondrial (ATP-binding cassette Q9NR 6 ABCB10 transporter 10) (ABC transporter 10 protein) 738 TRUE FALSE FALSE FALSE TRUE FALSE (Mitochondrial ATP-binding cassette 2) (M- ABC2) ATP-binding cassette sub-family D member 3 P28288 ABCD3 (70 kDa peroxisomal membrane protein) 659 FALSE FALSE FALSE TRUE TRUE TRUE (PMP70) ATP-binding cassette sub-family E member 1 (2'-5'-oligoadenyiate~binding protein) P61221 ABCE1 599 FALSE F S F FALSE. FALSE (HuHP68) (RNase L inhibitor) (Ribonudease 4 inhibitor) (RNS4I) ATP-binding cassette sub-family F member 1 Q8NE71 ABCF1 (ATP-binding cassette 50) (TNF-aipha- 845 FALSE FALSE FALSE FALSE FALSE FALSE stimulated ABC protein)

ATP-binding cassette sub-family F member 2 Q9UG63 ABCF2 623 FALSE FALSE FALSE FALSE TRUE FALSE (iron-inhibited ABC transporter 2)

Q9NUQ8 ABCF3 ATP-binding cassette sub-family F member 3 709 FALSE FALSE TRUE FALSE FALSE FALSE ATP-citrate synthase (EC 2.3 3.8) (ATP-ciirate P53396 ACLY (pro-S-)-lyase) (ACL) (Citrate cleavage 1101 FALSE FALSE FALSE FALSE FALSE FALSE enzyme) ATP-dependent 6-phosphofructokinase, liver type (ATP-PFK) (PFK-L) (EC 2 7.1. 1 ) (6- P17858 PFKL phosphofructokinase type B) (Phosphofructo-1- 780 TRUE TRUE FALSE TRUE FALSE TRUE kinase isozyme B) (PFK-B) (Phosphohexokinase) ATP-dependent 6-phosphofructokinase, platelet type (ATP-PFK) (PFK-P) (EC QQ1813 PFKP 2.7.1 . 1) (6-phosphofafctokinase type C) 784 FALSE FALSE FALSE FALSE FALSE FALSE (Phosphofructo-1 -kinase isozyme C) (PFK-C) (Phosphohexokinase) ATP-dependent C p protease ATP-binding 076031 CLPX Θ33 F L3 Ε A Ξ F L F Ε FA Ξ FAL EE subunit cipX-like, mitochondrial ATP-dependent Clp protease proteolytic Q16740 CLPP subunit, mitochondrial (EC 3.4.21 .92) 277 FALSE FALSE FALSE FALSE FALSE FALSE (Endopeptidase Clp) ATP-dependent DNA helicase Q 1 (EC 3.6.4.12) (DNA helicase, RecQ-like type 1) P46063 RECQL 649 FALSE FALSE FALSE TRUE FALSE TRUE (RecQ1) (DNA-dependent ATPase Q1) (RecQ protein-like 1) ATP-dependent RNA helicase A (RHA) (EC Q0821 DHX9 3.6.4.13) (DEAH box protein 9) (Leukophysin) 1270 FALSE FALSE FALSE FALSE FALSE FALSE (LKP) (Nuclear DNA helicase ) (NDH I )

ATP-dependent RNA helicase DDX1 (EC Q92499 DDX1 3.6.4.13) (DEAD box protein 1) (DEAD box 740 FALSE FALSE FALSE FALSE FALSE FALSE protein retinoblastoma) (DBP-RB) ATP-dependent RNA helicase DDX18 (EC Q9NVP1 DDX18 3.6.4.13) (DEAD box protein 18) ( yc- 670 TRUE TRUE TRUE FALSE FALSE FALSE regulated DEAD box proiein) (MrDb) ATP-dependent RNA helicase DDX19A (EC Q9NUU7 DDX19A 3.6.4.13) (DDX19-like proiein) (DEAD box 478 FALSE FALSE FALSE FALSE FALSE FALSE protein 19A) ATP-dependent RNA heiicase DDX24 (EC Q9GZR7 DDX24 859 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.4 13) (DEAD box protein 24) ATP-dependent RNA heiicase DDX39A (EC 000148 DDX39A 3.6.4 13) (DEAD box protein 39) (Nuclear 427 FALSE FALSE FALSE FALSE FALSE FALSE RNA heiicase URH49) ATP-dependent RNA heiicase DDX3X (EC 3.6.4.13) (DEAD box protein 3 , X- 000571 DDX3X 662 FALSE FALSE FALSE FALSE FALSE FALSE chromosomai) (DEAD box, X isoform) (Helicase-like protein 2) (HLP2) ATP-dependent RNA heiicase DDX42 (EC 3.6.4.13) (DEAD box protein 42) (RNA helicase-like protein) (RHELP) (RNA helicase- Q86XP3 DDX42 938 TRUE TRUE FALSE FALSE F F related protein) (RNAHP) (SF3b DEAD box protein) (Splicing factor 3B~associated 125 kDa protein) (SF3b125) ATP-dependent RNA heiicase DDX50 (EC Q9BQ39 DDX50 3.6.4.13) (DEAD box protein 50) (Gu-beta) 737 FALSE TRUE FALSE TRUE TRUE FALSE (Nucleolar protein Gu2) ATP-dependent RNA heiicase DDX51 (EC Q8N8A6 DDX51 666 TRUE FALSE FALSE TRUE TRUE TRUE 3.6.4.13) (DEAD box protein 51) ATP-dependent RNA heiicase DDX54 (EC 3.6.4.13) (ATP-dependent RNA heiicase Q8TDD1 DDX54 881 FALSE FALSE FALSE TRUE FALSE FALSE DP97) (DEAD box RNA heiicase 97 kDa) (DEAD box protein 54) ATP-dependent RNA heiicase DDX55 (EC Q8NHQ9 DDX55 600 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.4.13) (DEAD box protein 55) ATP-dependent RNA heiicase DHX29 (EC Q7Z478 DHX29 3.6.4.13) (DEAH box protein 29) (Nucleic acid 1369 FALSE FALSE FALSE FALSE FALSE FALSE heiicase DDXx) ATP-dependent RNA heiicase DHX36 (EC 3.6.4.12) (EC 3.6.4.13) (DEAH box protein 36) Q9H2U1 DHX36 (G4-resolvase 1) (G4R1) (MLE-like protein 1) 1008 FALSE FALSE FALSE TRUE TRUE TRUE (RNA heiicase associated with AU-rich element ARE) ATPase ASNA1 (EC 3.6.-.-) (Arsenical pump- driving ATPase) (Arsenite-stimuiated ATPase) 043681 ASNA1 348 TRUE FALSE FALSE FALSE TRUE FALSE (Transmembrane domain recognition complex 40 kDa ATPase subunii) (hARSA-l) (hASNA-l)

ATPase family AAA domain-containing protein Q9NVI7 ATAD3A 634 FALSE FALSE FALSE TRU E TRUE TRUE 3A ATPase family AAA domain-containing protein Q5T9A4 ATAD3B 648 FALSE FALSE FALSE FALSE TRUE FALSE 3B (AAA-TOB3) B-ce receptor-associated protein 3 1 (BCR- associated protein 3 1) (Bap31 ) (6C6-AG P51 572 BCAP31 246 FALSE FALSE FALSE FALSE FALSE FALSE tumor-associated antigen) (Protein CD ) (p28)

BAG family molecular chaperone regulator 2 09581 6 BAG2 2 11 TRUE FALSE FALSE FALSE FALSE FALSE (BAG-2) (Bcl-2-associated athanogene 2)

BAG family molecular chaperone regulator 5 Q9UL1 5 BAGS 447 FALSE FALSE FALSE FALSE FALSE FALSE •J\ (BAG-5) (Bci-2-associated athanogene 5)

Band 4 .1-like protein 2 (Generally expressed n EPB41 L2 1005 FALSE S F . 3 E TRU E TRUE TRUE protein 4 .1) (4. 1G) Barrier~to-autoinf egration factor (Breakpoint duster region protein 1) [Cleaved into: Barrier- 075531 BANF1 89 FALSE TRUE FALSE TRU E TRUE TRUE to-autointegration factor, N-terminally processed] Basic leucine zipper and W 2 domain- Q7L1 Q6 BZW1 4 19 FALSE FALSE FALSE FALSE FALSE FALSE containing protein 1 (Protein Orf) Basic leucine zipper and W 2 domain- Q9Y6E2 BZW2 4 19 TRUE TRUE TRUE TRUE TRUE TRUE containing protein 2

Basigin (5F7) (Collagenase stimulatory factor) (Extracellular matrix metalloproteinase inducer) (E PRIN) (Leukocyte activation P3561 3 385 FALSE FALSE FALSE TRU E FALSE TRUE antigen M6) (OK blood group antigen) (Tumor cell-derived collagenase stimulatory factor) (TCSF) (CD antigen CD1 47) Q9NYF8 BCLAF1 Bc!-2-associated transcription factor 1 (Btf) 920 FALSE FALSE FALSE FALSE FALSE FALSE

Bifunctionai 3'-phosphoadenosine 5'- phosphosulfate synthase 1 (PAPS synihase 1) (PAPSS 1) (Su!furyiase kinase 1) (SK 1) (SK1) [Includes: Sulfate adenyiyitransferase (EC 2.7 7.4) (ATP-sulfurylase) (Sulfate 043252 PAPSS1 adenylate transferase) (SAT); Adenylyl-sulfate 624 FALSE FALSE FALSE FALSE FALSE FALSE kinase (EC 2.7.1 .25) (3'-pbosphoadenosine-5'- phosphosulfate synthase) (APS kinase) (Adenosine- 5'-phosphosulfate 3'- phosphotransferase) (Adenyiyisulfate 3'- phosphotransferase)]

Bifunctionai epoxide hydrolase 2 [Includes: Cytosolic epoxide hydrolase 2 (CEH) (EC P34913 EPHX2 3.3.2.10) (Epoxide hydratase) (Soluble 555 FALSE FALSE FALSE FALSE FALSE FALSE epoxide hydrolase) (SEH); Lipid-phosphate phosphatase (EC 3.1 .3.76)] Bifunctionai glutamate/proline-tRNA ligase (Bifunctionai aminoacyl-tRNA synthetase) (Cell proliferation-inducing gene 32 protein) (G utama y -pro y -tRNA synthetase) [Includes: P07814 EPRS 1512 FALSE FALSE FALSE FALSE FALSE FALSE Glutamate-tRNA ligase (EC 6.1 . 1 .17) (Glutamyl-tRNA synthetase) (GluRS); Proiine- tRNA ligase (EC 6 . .1.15) (Prolyl-tRNA synthetase)] Bifunctionai methylenetetrahydrofolate dehydrogenase/cyciohydrolase, mitochondrial [Includes: NAD-dependent P13995 MTHFD2 350 FALSE TRUE FALSE FALSE FALSE FALSE methylenetetrahydrofolate dehydrogenase (EC 1.5.1 .15); Methenyltetrahydrofolate cyciohydrolase (EC 3.5.4.9)] BifLfnctiona! pLfrine biosynthesis protein PURH [Cleaved into: Bifunctional purine biosynthesis protein PURH, N-ferminaliy processed] [includes: Phosphoribosylaminoimidazolecarboxamide P31939 AT!C 592 FALSE TRUE TRUE FALSE FALSE FALSE formyltransferase (EC 2 1.2.3) (5- aminoimidazole-4-carboxamide ribonucleotide formyltransferase) (A!CAR transformylase); MP cydohydro!ase (EC 3.5.4.10) (ATIC) (IMP synthase) (Inosinicase)]

Biliverdin reductase A (BVR A) (EC 1.3.1 .24) P53004 BLVRA 296 FALSE FALSE FALSE FALSE FALSE FALSE (Biliverdin-iX aipha-reductase) Bleomycin hydrolase (BH) (BLM hydrolase) Q13867 BLMH 455 FALSE FALSE FALSE TRUE FALSE TRUE (BMH) (EC 3.4.22.40) Q9H3K6 BOLA2 Bo A- ike protein 2 86 FALSE FALSE FALSE TRUE TRUE TRUE Branched-chain-amino-acid aminotransferase, P54687 BCAT1 cytosolic (BCAT(c)) (EC 2.6.1 .42) (Protein 386 FALSE FALSE FALSE TRUE TRUE FALSE -4 ECA39) BRCA2 and CDKNIA-interacting protein (P21- Q9P287 BCCiP and CDK-associated protein 1) (Protein TOK- 314 TRUE FALSE FALSE FALSE TRUE TRUE 1) Brefeldin A-inhibited guanine nucleotide- exchange protein 1 (Brefeldin A-inhibited GEP 1) (ADP-ribosylation factor guanine nucleotide- Q9Y6D6 ARFGEF1 1849 FALSE S F . 3 E FALSE TRUE TRUE exchange factor 1) (p200 ARF guanine nucleotide exchange factor) (p200 ARF- GEP1) BRI3-binding protein (13-binding protein) Q8WY22 BRI3BP (Cervical cancer 1 proto-oncogene-binding 251 FALSE FALSE TRUE FALSE FALSE FALSE protein KG19) (HCCRBP-1) BR SC and BRCA1-A complex member 1 (Mediator of RAP80 interactions and targeting Q9NWV8 BABAM1 329 FALSE FALSE FALSE TRUE FALSE FALSE subunit of 40 kDa) (New component of the BRCA1-A complex) BR01 domain-containing protein BROX Q5VW32 BROX (BR01 domain- and CAAX motif-containing 4 11 FALSE FALSE FALSE TRUE FALSE FALSE protein) Q9NW68 BSDC1 BSD domain-containing protein 1 430 TRUE FALSE FALSE FALSE FALSE FALSE Q 3895 BYSL Bystin 437 FALSE TRUE FALSE FALSE FALSE FALSE C-1-tetrahydrofoiate synthase, cytoplasmic (C1-THF synthase) [Cleaved into: C-1- tetrahydrofolate synthase, cytoplasmic, N- terminally processed] [Includes: P 1 1586 T HFD1 Meihyleneietrahydrofolate dehydrogenase 935 FALSE FALSE FALSE FALSE FALSE FALSE (EC 1.5.1 .5); Methenyltetrahydrofolate cyciohydroiase (EC 3.5.4.9); Formyltetrahydrofolate synthetase (EC 6.3.4.3)]

C-Jun-amino-terminal kinase-interacting proiein 4 (JIP-4) (JNK-interacting protein 4) (Cancer/testis antigen 89) (CT89) (Human

0 lung cancer oncogene 6 protein) (HLC-6) (JNK-associaied !eucine-zipper protein) (JLP) 060271 SPAG9 (Mitogen-activated protein kinase 8-interacting 1321 FALSE FALSE FALSE FALSE FALSE FALSE protein 4) (Proliferation-inducing protein 6) (Proiein highly expressed in testis) (PHET) (Sperm surface protein) (Sperm-associated antigen 9) (Sperm-specific protein) (Sunday driver 1)

C-terminal-binding protein 1 (CtBP1) (EC Q13363 CTBP1 440 FALSE FALSE FALSE TRUE FALSE FALSE 1. 1 . 1 .-) CAAX prenyl protease 1 homo!og (EC 3.4.24.84) (Farnesylated proteins-converting 075844 enzyme 1) (FACE-1) (Prenyl protein-specific 475 FALSE FALSE FALSE FALSE TRUE FALSE endoprotease 1) (Zinc meiaiioproteinase Ste24 homolog) CAD protein [Includes: Giutamine-dependent carbamoyl-phosphate synthase (EC 6.3 5.5); P27708 CAD 2225 FALSE FALSE FALSE FALSE FALSE FALSE Aspartate carbamoyltransferase (EC 2.1 .3.2); Dihydroorotase (EC 3.5.2.3)]

Calcium homeostasis endoplasmic reticulum Q8IWX8 CHERP protein (ERPROT 213-21) (SR-related CTD- 916 FALSE FALSE FALSE FALSE FALSE FALSE associated factor 6)

Calcium uptake protein 2 , mitochondrial (EF- Q8IYU8 CU2 434 FALSE FALSE FALSE FALSE FALSE FALSE hand domain-containing family member A1)

Calcium-binding mitochondrial carrier protein SLC25A1 Q75746 Aralarl (Mitochondrial aspartate glutamate 678 TRUE TRUE FALSE FALSE TRUE FALSE 2 carrier 1) (Solute carrier family 25 member 12)

Calcyclin-binding protein (CacyBP) (hCacyBP) Q9HB71 CACYBP (S100A6-binding protein) (Siah-interacting 228 FALSE FALSE FALSE FALSE FALSE FALSE protein) Calnexin (IPSO) (Major histocompatibility P27824 CANX complex class antigen-binding protein p88) 592 FALSE FALSE FALSE FALSE FALSE FALSE (p90) Calpain small subunit 1 (CSS1) (Calcium- activated neutral proteinase small subunit) (CANP small subunit) (Calcium-dependent P04632 CAPNS1 268 FALSE FALSE FALSE TRUE TRUE FALSE protease small subunit) (CDPS) (Calcium- dependent protease small subunit 1) (Calpain regulatory subunit)

Calpain-1 catalytic subunit (EC 3.4.22.52) (Calcium-activated neutral proteinase 1) CAPN1 (CANP 1) (Calpain mu-type) (Calpain-1 large 714 FALSE FALSE FALSE FALSE FALSE FALSE subunit) (Ceil proliferation-inducing gene 30 protein) (Ivlicromolar-calpain) (muCANP)

Calponin-2 (Calponin H2, smooth muscle) Q99439 CNN2 309 FALSE FALSE FALSE FALSE FALSE TRUE (Neutral calponin) Calreticu!in (CRP55) (Calregulin) P27797 CALR (Endoplasmic reticulum resident protein 60) 417 FALSE FALSE FALSE FALSE FALSE FALSE (ERp60) (HACBP) (grp60) cAMP-dependent protein kinase type l-alpha PRKAR1 o y s n (Tissue-specific P10644 extinguisher 1) (TSE1) [Cleaved into: cA P- 381 FALSE FALSE FALSE FALSE FALSE FALSE dependent protein kinase type i-aipha regulatory subunit, N-terminally processed] Cancer-related nucleoside-triphosphatase Q9BSD7 NTPCR (NTPase) (EC 3.6.1 .15) (Nucleoside 190 FALSE FALSE FALSE FALSE FALSE FALSE triphosphate phosphohydrolase)

Caprin-1 (Ceil cycle-associated protein 1) (Cytoplasmic activation- and proliferation- associated protein 1) (GPI-anchored Q14444 CAPRIN1 membrane protein 1) (GPI-anchored protein 709 FALSE FALSE FALSE FALSE FALSE FALSE p137) (GPI-p137) (p137GPI) (Membrane o o component chromosome 11 surface marker 1) (RNA granule protein 105)

Carnitine ©-palmitoyltransferase 1, liver isoform (CPT1-L) (EC 2.3.1 .21) (Carnitine O- P50416 CPT1A 773 FALSE FALSE FALSE FALSE FALSE FALSE palmitoyitransferase , liver isoform) (CPT ) (CPTI-L) (Carnitine palmitoyltransferase 1A)

Carnitine O-paimitoyltransferase 2 , P23786 CPT2 mitochondrial (EC 2.3.1 .21) (Carnitine 658 FALSE FALSE FALSE FALSE FALSE TRUE palmitoyltransferase II) (CPT ) Casein kinase isoform alpha (CKI-alpha) (EC P48729 CSNK1A1 337 FALSE FALSE FALSE FALSE FALSE FALSE 2.7.1 1.1) (CK1) Casein kinase II subunit alpha (CK II alpha) P68400 CSNK2A1 391 FALSE FALSE FALSE FALSE TRUE FALSE (EC 2 .7.1 1.1) Casein kinase II subunit alpha' (CK alpha') P19784 CSNK2A2 350 FALSE FALSE FALSE TRUE FALSE FALSE (EC 2.7.1 1.1) Casein kinase I subunit beta (CK beta) P67870 CSNK2B 215 FALSE FALSE FALSE FALSE FALSE FALSE (Phosvitin) (Protein G5a) P04040 CAT Cata!ase (EC 1. 1. .6) 527 FALSE FALSE FALSE FALSE FALSE FALSE

P21964 CO T Catechol O-methyitransferase (EC 2.1 . .6) 271 FALSE TRUE TRUE TRUE TRUE TRUE

Catenin alpha~1 (Alpha E~catenin) (Cadherin- P35221 CTNNA1 associated protein) (Renal carcinoma antigen 906 FALSE FALSE FALSE FALSE FALSE FALSE NY-REN-13) Cathepsin D (EC 3 4.23.5) [Cleaved into: P07339 CTSD Cathepsin D light chain; Cathepsin D heavy 412 FALSE FALSE FALSE FALSE FALSE FALSE chain] CCAAT/enhancer-binding protein zeta QQ3701 CEBPZ (CCAAT-box-binding transcription factor) 1054 TRUE TRUE TRUE FALSE TRUE FALSE (CBF) (CCAAT-binding factor) CCR4-NOT transcription complex subunit 1 (CCR4-associated factor 1) (Negative A5YKK6 CNOT1 2376 FALSE FALSE! TRUE FALSE TRUE regulator of transcription subunit 1 homolog) (NOT1 H) (hNOT1)

Q9H9A5 CNOT1Q CCR4-NOT transcription complex subunit 10 744 FALSE FALSE FALSE FALSE FA LSE FALSE

CD81 antigen (28 kDa cell surface protein TAPA-1) (Target of the antiproliferative P60033 CD81 236 FALSE FALSER L TRUE TRUE FALSE antibody 1) (Tetraspanin-28) (Tspan-28) (CD antigen CD81) CDGSH iron-sulfur domain-containing protein Q9NZ45 CISD1 108 FALSE FALSE FALSE TRUE TRUE TRUE 1 (MitoNEET) CDGSH iron-sulfur domain-containing protein 2 (Endoplasmic reticulum intermembrane Q8N5K1 CISD2 small protein) (MitoNEET-related 1 protein) 135 FALSE FALSE FALSE TRUE FALSE TRUE (Minerl) (Nutrient-deprivation autophagy factor- 1) (NAF-1) CDK5 regulatory subunit-associated protein 3 CD 5RA (CD 5 activator-binding protein CSS) Q96JB5 506 FALSE FALSE FALSE FALSE FALSE FALSE P3 (LXXLMeucine-zipper-containing ARF-binding protein) (Protein HSF-27) Cell cycle and apoptosis regulator protein 2 (Ceil division cycle and apoptosis regulator Q8N163 CCAR2 protein 2) (DBIRD complex subunit KIAA1967) 923 FALSE FALSE TRUE FALSE FALSE FALSE (Deleted in breast cancer gene 1 protein) (DBC-1) (DBC.1) (NET35) (p30 DBC)

Cell division control protein 42 homolog (G25K P60953 CDC42 191 FALSE FALSE FALSE FALSE FALSE FALSE GTP-binding protein) Cell division cycle 5-like protein (CdcS-iike Q99459 CDC5L 32 FALSE FALSE FALSE TRUE TRUE FALSE protein) (Pombe cdc5-reiated protein) Cell division cycle and apoptosis regulator protein 1 (Ceil cycle and apoptosis regulatory Q8IX12 CCAR1 1150 FALSE FALSE FALSE TRUE TRUE TRUE protein 1) (CARP-1) (Death inducer with SAP domain) Cell division cycle protein 23 homolog Q9UJX2 CDC23 (Anaphase-promoting complex subunit 8) 597 FALSE FALSE FALSE FALSE FALSEi TRUE (APC8) (Cyclosome subunit 8) Q9NX58 LYAR Cell growth-regulating nucleolar protein 379 TRUE TRUE FALSE TRUE TRUE FALSE Cellular nucleic acid-binding protein (CNBP) P62633 CNBP 177 FALSE FALSE! FALSE FALSE FA LS (Zinc finger protein 9) Centromere protein V (CENP-V) (Nuclear Q7Z7K6 CENPV 2 FALSE FALSE TRUE FALSE FALSE FALSE protein p30) (Proiine-rich protein 6) Centromere/kinetochore protein zw1 0 043264 ZW10 779 FALSE FALSE F L FALSE FALSE FALSE homolog

Ceramide synthase 2 (CerS2) (LAG1 longevity Q96G23 CERS2 assurance homolog 2) (SP260) (Tumor 380 FALSE TRUE TRUE FALSE TRUE TRUE metastasis-suppressor gene 1 protein)

Ceroid-lipofuscinosis neuronal protein 6 Q9NWW5 CLN6 3 11 FALSE TRUE FALSE FALSE FALSE FALSE (Protein CLN6) Charged multivesicular body protein 5 (Chromatin-modifying protein 5) (SNF7 Q9NZZ3 CH P5 domain-containing protein 2) (Vacuolar protein 219 FALSE FALSE FALSE FALSE FALSE FALSE sorting-associated protein 60) (Vps60) (hVps60) Chloride intracellular channel protein 1 (Chloride channel ABP) (Nuclear chloride ion 000299 CLIC1 FALSE FALSE FALSE FALSE FALSE FALSE channel 27) (NCC27) (Regulatory nuclear chloride ion channel protein) (hRNCC) Chloride intracellular channel protein 4 Q9Y696 CLIC4 (Intracellular chloride ion channel protein p64H1) Chromatin assembly factor 1 subunit B (CAF- 1 subunit B) (Chromatin assembly factor I p60 Q131 12 CHAF1 B 559 FALSE FALSE FALSE TRUE FALSE FALSE subunit) (CAF-I 60 Da subunit) (CAF-I p60) (M-phase phosphoprotein 7)

Chromatin target of PR T 1 protein (Friend of Q9Y3Y2 CHTOP PR T 1 protein) (Small arginine- and glycine- 248 FALSE FALSE FALSE FALSE FALSE FALSE rich protein) (SRAG) Chromobox protein homoiog 3 (HECH) o Q13185 CBX3 (Heterochromatin protein 1 homoiog gamma) 183 FALSE FALSE FALSE FALSE FALSE FALSE (HP1 gamma) (Modifier 2 protein)

Chromobox protein homoiog 5 (Antigen p25) P45973 CBX5 (Heterochromatin protein 1 homoiog alpha) 191 FALSE FALSE FALSE TRUE TRUE TRUE (HP1 alpha) Chromodomain-helicase-DNA-binding protein 014646 CHD1 1 (CHD-1) (EC 3.6.4.12) (ATP-dependent 1710 FALSE FALSE FALSE FALSE FALSE TRUE helicase CHD1) Chromodomain-helicase-DNA-binding protein 4 (CHD-4) (EC 3.6.4.12) (ATP-dependent Q14839 CHD4 1912 FALSE FALSE FALSE FALSE FALSE FALSE helicase CHD4) (Mi-2 autoantigen 218 kDa protein) (Mi2-beta) Chromodomain-helicase-DNA-binding proiein Q8TDI0 CHD5 5 (CHD-5) (EC 3.6.4.12) (ATP-dependent 1954 FALSE FALSE FALSE FALSE FALSE FALSE helicase CHD5) Cilia- and flagella-associated protein 20 (Basal Q9Y6A4 CFAP20 body up-regulated protein 22) (Transcription 193 FALSE FALSE FALSE FALSE FALSE FALSE factor B) Citrate synthase, mitochondrial (EC 2 3.3.1) 075390 CS 466 FALSE FALSE FALSE TRUE TRUE TRUE (Citrate (Si)-synthase) C!athrin heavy chain 1 (Clathrin heavy chain Q00610 CLTC 1675 FALSE FALSE FALSE FALSE FALSE FALSE on chromosome 17) (CLH-17) P09496 CLTA Clathrin light chain A (Lea) 248 FALSE FALSE FALSE FALSE FALSE FALSE Cleavage and polyadenylation specificity factor subunit 1 (Cleavage and Q10570 CPSF1 1443 FALSE FALSE FALSE FALSE FALSE FALSE polyadenylation specificity factor 160 kDa subunit) (CPSF 160 kDa subunit) Cleavage and polyadenylation specificity factor subunit 2 (Cleavage and Q9P2IQ CPSF2 782 FALSE FALSE FALSE FALSE FALSE FALSE polyadenylation specificity factor 100 kDa subunit) (CPSF 100 kDa subunit)

Cleavage and polyadenylation specificity factor subunit 3 (EC 3.1 .27.-) (Cleavage and Q9UKF6 CPSF3 polyadenylation specificity factor 73 kDa 684 FALSE TRUE FALSE TRUE FALSE FALSE subunit) (CPSF 73 kDa subunit) (mRNA 3'~ end-processing endonuclease CPSF-73)

Cleavage and polyadenylation specificity factor subunit 4 (Cleavage and polyadenylation specificity factor 30 kDa 095639 CPSF4 269 FALSE FALSE FALSE FALSE FALSE FALSE subunit) (CPSF 30 kDa subunit) (NS1 effector domain-binding protein 1) (Neb-1) (No arches homoiog) Cleavage and polyadenylation specificity factor subunit 5 (Cleavage and polyadenylation specificity factor 25 kDa 043809 NUDT21 subunit) (CFIm25) (CPSF 25 kDa subunit) 227 FALSE FALSE FALSE TRUE TRUE TRUE (Nucleoside diphosphate-linked moiety X motif 21) (Nudix motif 21) (Pre-mRNA cleavage factor Im 25 kDa subunit) Cleavage and polyadenylation specificity factor subunit 8 (Cleavage and polyadenylation specificity factor 68 kDa Q16630 CPSF6 551 FALSE FALSE FALSE FALSE FALSE FALSE subunit) (CFIm68) (CPSF 68 kDa subunit) (Pre-mRNA cleavage factor m 68 kDa subunit) (Protein HPBRII-4/7) Cleavage and polyadenylation specificity factor subunit 7 (Cleavage and polyadenylation specificity factor 59 kDa Q8N684 CPSF7 471 FALSE FALSE FALSE FALSE FALSE FALSE subunit) (CFim59) (CPSF 59 kDa subunit) (Pre-mRNA cleavage factor m 59 kDa subunit)

Cleavage stimulation factor subunit 2 (CF-1 64 kDa subunit) (Cleavage stimulation factor 64 577 FALSE FALSE FALSE TRUE FALSE FALSE kDa subunit) (CSTF 64 kDa subunit) (CstF-64)

Cleavage stimulation factor subunit 3 (CF-1 77 S Q12996 CSTF3 kDa subunit) (Cleavage stimulation factor 77 717 FALSE FALSE FALSE TRUE TRUE FALSE kDa subunit) (CSTF 77 kDa subunit) (CstF-77)

096005 CLPT 1 Cleft lip and palate transmembrane protein 1 669 FALSE FALSE FALSE TRUE FALSE TRUE

Cleft lip and palate transmembrane protein 1- Q96KA5 CLPTM1 L like protein (CLPTM1-like protein) (Cispiatin 538 FALSE FALSE FALSE FALSE FALSE FALSE resistance-related protein 9) (CRR9p)

CLIP-associating protein 1 (Cytoplasmic linker- Q7Z460 CLASP1 associated protein 1) (Multiple asters homolog 1538 TRUE FALSE FALSE FALSE TRUE FALSE 1) (Protein Orbit homolog 1) (hOrbitl) CLIP-associating protein 2 (Cytoplasmic iinker- 075122 CLASP2 associated protein 2) (Protein Orbit homolog 1294 FALSE FALSE FALSE FALSE FALSE TRUE 2) (hOrbit2) 075153 CLUH Clustered mitochondria protein homolog 1309 FALSE FALSE FALSE FALSE FALSE FALSE Coatomer subunit alpha (Alpha-coat protein) (Alpha-COP) (HEP-COP) (HEPCOP) [Cleaved P53621 COPA 1224 FALSE FALSE FALSE FALSE FALSE FALSE into: Xenin (Xenopsin-related peptide); Proxenin] Coatomer subunit beta (Beta-coat proiein) P53618 COPB1 953 FALSE FALSE FALSE TRUE TRUE TRUE (Beta-COP) Coatomer subunit beta' (Beta'-coat protein) P35606 COPB2 906 FALSE FALSE FALSE FALSE FALSE FALSE (Beta'-COP) (p102) Coatomer subunit delta (Archain) (Delta-coat P48444 ARCN1 5 11 TRUE TRUE FALSE TRUE FALSE TRUE protein) (Delta-COP) Coatomer subunit epsilon (Epsilon-coat 014579 COPE 3 8 TRUE FALSE FALSE FALSE FALSE FALSE protein) (Epsilon-COP) Coatomer subunit gamma-1 (Gamma-1 -coat Q9Y678 COPG1 874 FALSE FALSE FALSE TRUE FALSE TRUE protein) (Gamma-1-COP) Coatomer subunit gamma-2 (Gamma-2-coat Q9UBF2 COPG2 871 FALSE FALSE TRUE FALSE FALSE TRUE protein) (Gamma-2-COP) Cofilin-1 (18 kDa phosphoprotein) (p18) P23528 CFL1 166 FALSE FALSE FALSE FALSE FALSE FALSE (Cofilin, non-muscle isoform) o Cohesin subunit SA-2 (SCC3 homolog 2) Q8N3U4 STAG2 1231 FALSE FALSE FALSE FALSE FALSE FALSE (Stromal antigen 2) Q96A33 CCDC47 Coiled-coil domain-containing protein 47 483 FALSE FALSE FALSE ∆ TRUE

Cold shock domain-containing proiein E 1 (N- 075534 H 798 FALSE FALSE FALSE TRUE TRUE TRUE ras upstream gene protein) (Protein UNR)

Complement component 1 Q subcomponent- binding protein, mitochondrial (ASF/SF2- associated protein p32) (Glycoprotein FALSE FALSE FALSE FALSE FALSE FALSE gClqBP) (C1qBP) (Hyaiuronan-binding protein 1) (Mitochondrial matrix protein p32) (gC1q~R protein) (p33) Condensin complex subunit 1 (Chromosome condensation-related SMC-associated protein Q15021 NCAPD2 1) (Chromosome-associated protein D2) 1401 FALSE FALSE FALSE FALSE FALSE FALSE (hCAP-D2) (Non-SMC condensin i complex subunit D2) (XCAP-D2 homoiog)

Condensin complex subunit 2 (Barren homoiog protein 1) (Chromosome-associatec Q15003 NCAPH 741 TRUE TRUE FALSE FALSE TRUE FALSE protein H) (hCAP-H) (Non-SMC condensin i complex subunit H) (XCAP-H homoiog)

Condensin complex subunit 3 (Chromosome- associated protein G) (Condensin subunit Q9BPX3 NCAPG CAP-G) (hCAP-G) (Melanoma antigen NY- 1015 TRUE TRUE FALSE TRUE FALSE FALSE MEL-3) (Non-SMC condensin complex subunit G) (XCAP-G homoiog) o Condensin-2 complex subunit G2 (Chromosome-associated protein G2) (CAP- Q86XI2 1143 FALSE FALSE FALSE FALSE TRUE FALSE G2) (hCAP~G2) (Leucine zipper protein 5) (Non-SMC condensin complex subunit G2)

Constitutive coactivator of PPAR-gamma-like Q9NZB2 FA ]120A protein 1 (Oxidative stress-associated Src 1118 FALSE FALSE FALSE FALSE FALSE FALSE activator) (Protein FAM12QA) COP9 signalosome complex subunit 1 (SGN1) (Signa!osome subunit 1) (G protein pathway Q13098 GPS1 491 FALSE FALSE FALSE FALSE FALSE FALSE suppressor 1) (GPS-1) (JAB1 -containing signalosome subunit 1) (Protein MFH)

COP9 signalosome complex subunit 2 (SGN2) (Signalosome subunit 2) (Alien homoiog) P61201 COPS2 (JAB1 -containing signalosome subunit 2) 443 FALSE FALSE FALSE FALSE FALSE TRUE (Thyroid receptor-interacting protein 15) (TR- interacting protein 15) (TRIP- 15) COP9 signalosome complex subunit 4 (SGN4) Q9BT78 COPS4 (Signalosome subunit 4) (JAB1 -containing 406 TRUE FALSE FALSE FALSE FALSE TRUE signalosome subunit 4) COP9 signalosome complex subunit 7b Q9H9Q2 COPS7B (SGN7b) (Signalosome subunit 7b) (JAB1- 264 FALSE FALSE FALSE FALSE FALSE FALSE containing signalosome subunit 7b) Q99829 CPNE1 Copine-1 (Chromobindin 17) (Copine ) 537 FALSE FALSE FALSE FALSE FALSE FALSE 075131 CPNE3 Copine-3 (Copine ill) 537 FALSE FALSE FALSE FALSE FALSE TRUE Core bistone macro-H2A.1 (Histone macroH2A1) (mH2A1) (Histone H2A.y) 075367 H2AFY 3 F S ! FA L E! F ! F S FA L E! FALSE (H2A/y) (Medulioblastoma antigen U- B- 50.205)

Core-binding factor subunit beta (CBF-beta) (Polyomavirus enhancer-binding protein 2 Q13951 CBFB beta subunit) (PEA2-beta) (PEBP2-beta) (SL3- 182 TRUE TRUE FALSE FALSE FALSE FALSE 3 enhancer factor 1 subunit beta) (SL3/AKV core-binding factor beta subunit) o Coronin-1A (Coronin-like protein A) (Clipin-A) P31 146 COR01A (Coronin-like protein p57) (Tryptophan 461 FALSE FALSE FALSE FALSE FALSE FALSE aspartate-containing coat protein) (TACO) Q9ULV4 CORQ1C Coronin-1C (Coronin-3) (hCRNN4) 474 FALSE FALSE FALSE FALSE FALSE FALSE Coronin-7 (Crn7) (70 kDa W D repeat tumor P57737 CORQ7 925 TRUE TRUE TRUE FALSE FALSE FALSE rejection antigen homolog) P46109 CRKL Crk-like protein 303 FALSE FALSE FALSE TRUE FALSE FALSE CTP synthase 1 (EC 6.3.4 2) (CTP synthetase P17812 CTPS1 591 FALSE FALSE FALSE FALSE FALSE FALSE 1) (UTP-ammonia ligase 1) CUGBP E av- ike family member 1 (CELF-1) (5 kDa nuclear polyadenylated RNA-binding protein) (Bruno-like protein 2) (CUG triplet repeat RNA-binding protein 1) (CUG-BP1) Q92879 CELF1 (CUG-BP- and ETR-3-iike factor 1) 486 FALSE FALSE FALSE TRUE FALSE FALSE (Deadenylation factor CUG-BP) (Embryo deadenyiation element-binding protein homolog) (EDEN-BP bomolog) (RNA-binding protein BRUNOL-2) Q13617 CUL2 Culiin-2 (CUL-2) 745 FALSE FALSE FALSE TRUE FALSE FALSE Q13618 CUL3 Culiin-3 (CUL-3) 768 FALSE TRUE TRUE FALSE FALSE FALSE Q13619 CUL4A Culiin-4A (CUL-4A) 759 FALSE FALSE FALSE TRUE TRUE FALSE Q13620 CUL4B Culiin-4B (CUL-4B) 913 FALSE FALSE FALSE TRUE TRUE FALSE Cullin-associated NEDDS-dissociated protein 1 (Cullin-associated and neddylation- Q86VP6 CAND1 dissociated protein 1) (TBP-interacting protein 1230 FALSE FALSE FALSE FALSE FALSE FALSE of 2 kDa A) (TBP-interacting protein 120A) (p120 CAND1) o Cyciin-dependent kinase 1 (CDK1) (EC 2.7.1 1.22) (EC 2.7.1 1.23) (Cell division control P06493 CDK1 297 FALSE FALSE FALSE FALSE FALSE FALSE protein 2 homolog) (Cell division protein kinase 1) (p34 protein kinase) Cyciin-dependent kinase 12 (EC 2.7.1 1.22) (EC 2.7.1 1.23) (Cdc2-related kinase, arginine/serine-rich) (CrkRS) (Cell division Q9NYV4 CDK12 1490 FALSE FALSE FALSE FALSE FALSE FALSE cycle 2-related protein kinase 7) (CDC2- related protein kinase 7) (Cell division protein kinase 12) (hCDK12)

Cyclin-dependent kinase 6 (EC 2.7.1 .22) Q00534 CDK6 (Cell division protein kinase 6) 326 FALSE FALSE FALSE FALSE FALSE FALSE (Serine/threonine-protein kinase PLSTIRE) Cyciin-dependent kinase 9 (EC 2.7.1 .22) (EC 2.7.1 1.23) (C-2K) (Cei division cycle 2-!ike protein kinase 4) (Cell division protein kinase P50750 CDK9 37; FALSE FALSE FALSE FALSE FALSE FALSE 9) (Serine/threonine-protein kinase PITALRE) (Tat-associated kinase complex catalytic subunit) Cysteine and histidine-rich domain-containing CHORDC protein 1 (CHORD domain-containing protein Q9UHD1 33; FALSE FALSE FALSE FALSE FALSE FALSE 1 1) (CHORD-containing protein 1) (CHP-1) (Protein morgana) Cysteine protease ATG4B (EC 3.4.22.-) (AUT- like 1 cysteine endopeptidase) (Autophagin-1) Q9Y4P1 ATG4B (Autophagy-related cysteine endopeptidase 1) 393 FALSE FALSE FALSE FALSE FALSE FALSE (Autophagy-related protein 4 homoiog B) (hAPG4B) Cysteine-tRNA ligase, cytoplasmic (EC P49589 CARS 6.1 . 1 .16) (Cysteinyl-tRNA synthetase) 748 TRUE FALSE FALSE TRUE TRUE FALSE (CysRS) Cysteine-rich C-terminal protein 1 (Protein Q9UGL9 CRCT1 99 FALSE FALSE FALSE FALSE FALSE FALSE NICE-1) Cytochrome b~c1 complex subunit 1, mitochondrial (Complex Hi subunit 1) (Core P31930 UQCRC1 480 FALSE FALSE FALSE FALSE FALSE FALSE protein ) (Ubiquinol-cytochrome-c reductase complex core protein 1) Cytochrome b~ complex subunit 2 , mitochondrial (Complex HI subunit 2) (Core P22695 UQCRC2 453 FALSE FALSE FALSE FALSE FALSE FALSE protein II) (Ubiquinol-cytochrome-c reductase complex core protein 2)

Cytochrome b-c1 complex subunit 8 (Complex

HI subunit 8) (Complex 1 1 subunit VIII) (Ubiquinoi-cytochrome c reductase complex 014949 UQCRQ 32 FALSE FALSE FALSE FALSE TRUE FALSE 9.5 kDa protein) (Ubiquinoi-cytochrome c reductase complex ubiquinone-binding protein QP-C) Cytochrome b- complex subunit 9 (Complex H subunit 9) (Complex III subunit X) Q9UDW1 UQCR10 (Cytochrome non-heme 7 kDa protein) 63 FALSE FALSE FALSE FALSE FALSE FALSE (Ubiquinol-cytochrome c reductase complex 7.2 kDa protein) Cytochrome b- complex subunit Rieske, mitochondrial (EC 1.10.2 2) (Complex III subunit 5) (Cytochrome b- complex subunit 5) (Rieske iron-sulfur protein) (RISP) UQCRFS (Ubiquinol-cytochrome c reductase iron-sulfur 274 TRUE TRUE FALSE TRUE TRUE FALSE 1 subunit) [Cleaved into: Cytochrome b- complex subunit 11 (Complex III subunit IX) (Ubiquinol-cytochrome c reductase 8 kDa protein)] Cytochrome b5 type B (Cytochrome b5 outer 043169 CYB5B 146 F ! FALSE FAL TRUE TRUE TRUE mitochondrial membrane isoform) P99999 CYCS Cytochrome c 105 FALSE FALSE FALSE TRUE FALSE TRUE Q5R 5 COX20 Cytochrome c oxidase protein 20 homolog 118 FALSE TRUE FALSE FALSE FALSE FALSE Cytochrome c oxidase subunit 2 (Cytochrome P00403 T-CG2 227 TRUE TRUE FALSE F LSE FALSE FALSE c oxidase polypeptide II) Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (Cytochrome c oxidase P13073 COX4I1 169 FALSE FAL E FAL FALSE FALSE polypeptide IV) (Cytochrome c oxidase subunit IV isoform 1) (COX I -1) Cytochrome c oxidase subunit 5A, P20674 COX5A mitochondrial (Cytochrome c oxidase 150 FALSE FALSE FALSE FALSE FALSE FALSE polypeptide Va) Cytochrome c oxidase subunit 6B1 P14854 COX6B1 (Cytochrome c oxidase subunit V b isoform 1) 86 FALSE FALSE FALSE FALSE FALSE FALSE (COX Ib-1) Cytochrome c oxidase subunit 7C, P15954 COX7C mitochondrial (Cytochrome c oxidase 63 FALSE FALSE FALSE FALSE FALSE FALSE polypeptide Vile) Cytochrome c-type heme lyase (CCHL) (EC P53701 HCCS 268 TRUE TRUE FALSE FALSE TRUE FALSE 4.4.1 .17) (Holocytochrome c-type synthase) Cytochrome c 1, heme protein, mitochondrial (Complex i subunit 4) (Complex HI subunit P08574 IV) (Cytochrome b-c1 complex subunit 4) 325 FALSE FALSE FALSE FALSE FALSE FALSE (Ubiquinoi-cytochrome-c reductase complex cytochrome c 1 subunit) (Cytochrome c-1)

Cytokine receptor-like factor 3 (Cytokine receptor-like molecule 9) (CREME-9) Q8IU18 CRLF3 442 FALSE FALSE FALSE FALSE TRUE FALSE (Cytokine receptor-related protein 4) (Type cytokine receptor-like factor p48)

Cytoplasmic aconitate hydratase (Aconitase) (EC 4.2.1 .3) (Citrate hydro-iyase) (Ferritin P21399 AC01 repressor protein) (Iron regulatory protein 1) 889 FALSE FALSE FALSE FALSE FALSE FALSE (IRP1) (Iron-responsive element-binding protein 1) (IRE-BP 1)

Cytoplasmic dynein 1 heavy chain 1 DY C H Q14204 (Cytoplasmic dynein heavy chain 1) (Dynein 4646 FALSE FALSE FALSE FALSE FALSE FALSE 1 heavy chain, cytosoiic) Cytoplasmic dynein 1 intermediate chain 2 (Cytoplasmic dynein intermediate chain 2) Q13409 DYNC1 I2 638 FALSE FALSE FALSE FALSE FALSE FALSE (Dynein intermediate chain 2 , cytosoiic) (DH IC-2) Cytoplasmic dynein 1 light intermediate chain DYNC1 L I Q9Y6G9 1 (LIC1) (Dynein light chain A) (DLC-A) 523 TRUE FALSE TRUE TRUE FALSE FALSE 1 (Dynein light intermediate chain 1, cytosoiic)

Cytoplasmic FMR1-interacting protein 1 Q7L576 CYFIP1 (Specifically Rac1 -associated protein 1) (Sra- 1253 FALSE FALSE FALSE FALSE FALSE FALSE 1) (p140sra-1) Cytoskeleton-associated protein 5 (Colonic CKAP5 and hepatic tumor overexpressed gene 2032 FALSE TRUE FALSE TRUE TRUE TRUE protein) (Ch-TOG) Cytosol aminopeptidase (EC 3 4 . .1) (Leucine amino-peptidase 3) (LAP-3) (Leucy! P28838 LAPS aminopeptidase) (Peptidase S) (Proline 5 19 FALSE FALSE FALSE TRU E TRUE FALSE aminopeptidase) (EC 3.4. 1.5) (Prolyl aminopeptidase)

Cytosolic acyl coenzyme A thioester hydrolase (EC 3 .1.2.2) (Acyl-CoA thioesterase 7) (Brain OQ01 54 ACOT7 380 FALSE FALSE FALSE FALSE FALSE FALSE acyl-CoA hydrolase) (BACH) (CTE-l la) (CTE- ) (Long chain acyl-CoA thioester hydrolase)

Cytosolic Fe-S cluster assembly factor NUBP2 Q9Y5Y2 NUBP2 271 FALSE FALSE FALSE FALSE FALSE FALSE (Nucleotide-binding protein 2) (NBP 2)

Cytosolic non-specific dipeptidase (EC 3.4. 13 .18) (CNDP dipeptidase 2) (Carnosine Q96KP4 CNDP2 dipeptidase II) (Epididymis secretory protein Li 475 FALSE S F . 3 E FALSE FALSE FALSE 13) (G uta ate carboxypeptidase-iike protein 1) (Peptidase A)

Cytosolic purine 5'-nucleotidase (EC 3 .1.3.5) P49902 NT5C2 561 FALSE F S F . 3 E FALSE FALSE FALSE (Cytosolic 5'-nucleotidase II) D-3-phosphogiycerate dehydrogenase (3- PGDH) (EC 1.1.1.95) (2-oxoglutarafe 0431 75 PHGDH 533 FALSE FALSE FALSE FALSE FALSE FALSE reductase) (EC 1.1 1.399) (Malate dehydrogenase) (EC 1.1.1.37)

D-tyrosyl-tRNA(Tyr) deacylase 1 (EC 3 .1.-.-) Q8TEA8 DTD1 (DNA-unwinding element-binding protein B) 209 FALSE FALSE FALSE FALSE FALSE FALSE (DUE-B) (Histidyl-tRNA synthase-related)

DAZ-associafed protein 1 (Deleted in Q96EP5 DAZAP1 407 FALSE FALSE FALSE TRU E TRUE TRUE azoospermia-associated protein 1)

DCN 1-!ike protein 1 (DCUN 1 domain- DCUN 1D containing protein 1) (Defective in cul in Q96GG9 259 FALSE FALSE FALSE FALSE FALSE FALSE 1 neddylation protein 1-like protein 1) (Squamous cell carcinoma-related oncogene) DDB1- and CUL4-associated factor 3 (WD Q9NV06 DCAF13 445 FALSE FALSE FALSE FALSE TRUE FALSE repeat and SOF domain-containing protein 1)

DDB1- and CUL4-associated factor 7 (WD P61962 DCAF7 repeat-containing protein 68) (WD repeat- 342 TRUE FALSE FALSE FALSE FALSE FALSE containing protein An1 1 homoiog) DDRG domain-containing protein 1 Q96HY6 DDRGK1 (Dashurin) (UFM1-binding and PCI domain- 314 FALSE FALSE FALSE FALSE TRUE TRUE containing protein 1)

Delta-1-pyrroline-5-carboxylate synthase (P5CS) (Aldehyde dehydrogenase family 18 member A1) [Includes: Glutamate 5-kinase ALDH18A (GK) (EC 2.7.2.1 1) (Gam a-g utamy kinase); 795 FALSE FALSE FALSE TRUE TRUE TRUE 1 Gamma-glutamyl phosphaie reductase (GPR) (EC 1.2.1 .41) (G!utamafe-5-semialdehyde dehydrogenase) (G!utamyl-gamma- semiaidehyde dehydrogenase)]

Delfa(24)-sterol reductase (EC 1.3.1 .72) (24- dehydrocholesterol reductase) (3-beta- Q15392 DHCR24 516 FALSE F L FALSE! TRUE TRUE TRUE hydroxysterol delta-24-reductase) (Diminuto/dwarfl homoiog) (Seladin-1) Delfa(3,5)-Delta(2,4)~dienoyl-CoA isomerase, Q1301 1 ECH1 328 FALSE FALSE FALSE FALSE FALSE FALSE mitochondrial (EC 5.3.3.-) Density-regulated protein (DRP) (Protein 043583 DENR DRP1) (Smooth muscle cell-associated 198 TRUE FALSE FALSE FALSE FALSE FALSE protein 3) (S A P 3) Deoxycytidylate deaminase (EC 3.5.4 12) P32321 DCTD 178 FALSE FALSE FALSE FALSE FALSE FALSE (dCMP deaminase)

Deoxyuridine 5'-triphosphate P33316 DUT nucieotidohydrolase, mitochondrial (dUTPase) 252 FALSE FALSE FALSE FALSE FALSE FALSE (EC 3.6.1 .23) (dUTP pyrophosphatase)

Desmogiein-1 (Cadherin family member 4) Q02413 (Desmosomal glycoprotein 1) (DG1) (DGI) 1049 FALSE FALSE! FALSE FALSE FALSE (Pemphigus fo!iaceus antigen) P60981 DSTN Des n (Actin-depolymerizing factor) (ADF) 165 FALSE FALSE FALSE TRUE TRUE TRUE Deve!opmentally-regulated GTP-binding protein 1 (DRG-1) (Neural precursor cell Q9Y295 367 FALSE FALSE FALSE FALSE FALSE FALSE expressed developmental^ down-regulated protein 3) (NEDD-3) Developmentaily-regulated GTP-binding P55039 DRG2 364 FALSE FALSE FALSE FALSE FALSE FALSE protein 2 (DRG-2) P00374 DHFR Dihydrofolate redLfctase (EC 1.5.1 .3) 187 FALSE FALSE FALSE FALSE FALSE FALSE Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1 .4) (Dihydrolipoamide P09622 39 FALSE FALSE FALSE FALSE FALSE FALSE dehydrogenase) (Glycine cleavage system L protein) Dihydrolipoyliysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial (EC 2.3.1 .12) (70 kDa mitochondrial autoantigen of primary biliary cirrhosis) (PBC) (Dihydrolipoamide P10515 DLAT 647 FALSE FALSE FALSE FALSE FALSE FALSE acetyltransferase component of pyruvate dehydrogenase complex) (M2 antigen complex 70 kDa subunit) (Pyruvate dehydrogenase complex component E2) (PDC- E2) (PDCE2)

Dihydrolipoyliysine-residue succinyliransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial (EC 2.3.1 .81) (2- P36957 DLST oxoglufarate dehydrogenase complex 453 TRUE FALSE FALSE FALSE FALSE FALSE component E2) (OGDC-E2) (Dihydrolipoamide succinyltransferase component of 2- oxoglutarate dehydrogenase complex) (E2K) Dipeptidyl peptidase 3 (EC 3.4.14.4) (Dipeptidyl aminopeptidase III) (Dipeptidyl Q9NY33 DPP3 737 TRUE FALSE FALSE FALSE FALSE FALSE arylamidase Hi) (Dipeptidyl peptidase III) (DPP III) (Enkephalinase B) 2-(3-arnino-3-carboxypropyl)histidine synthase subunit 2 (EC 2.5.1 .108) (Diphthamide biosynthesis protein 2) (Diphtheria toxin Q9BQC3 DPH2 489 FALSE FALSE FALSE FALSE FALSE FALSE resistance protein 2) (S-adenosyl-L- methionine: L-histidine 3-amino-3- carboxypropyitransferase 2) Disco-interacting protein 2 ho o og B (DIP2 Q9P265 DIP2B 1576 FALSE FALSE FALSE FALSE FALSE FALSE homolog B) DNA (cytosine-5)-methyltransferase 1 (Dnmtl) (EC 2.1 . 1 .37) (CXXC-type zinc finger protein P26358 DN T 1 1616 FALSE FALSE FALSE TRUE TRUE TRUE 9) (DNA methyltransferase Hsal) (DNA MTase Hsai) (M.Hsal) (MC T)

DNA damage-binding protein 1 (DDB p127 subunit) (DNA damage-binding protein a) (DDBa) (Damage-specific DNA-binding proiein 1) (HBV X-associated protein 1) (XAP-1) (UV- Q16531 DDB1 damaged DNA-binding factor) (UV-damaged 1140 FALSE FALSE FALSE TRUE TRUE TRUE DNA-binding protein 1) (UV-DDB 1) (XPE- binding factor) (XPE-BF) (Xeroderma pigmentosum group E-complementing protein) (XPCe)

P07992 ERCC1 DNA excision repair protein ERCC-1 297 FALSE FALSE FALSE FALSE FALSE FALSE

DNA ligase 1 (EC 6 5.1.1) (DNA ligase ) P18858 LIG1 919 FALSE FALSE FALSE FALSE FALSE FALSE (Polydeoxyribonudeotide synthase [ATP] 1)

DNA ligase 3 (EC 6 5.1.1) (DNA ligase III) P49916 LIG3 1009 TRUE FALSE FALSE TRUE TRUE TRUE (Polydeoxyribonudeotide synthase [ATP] 3)

DNA mismatch repair protein Mih1 ( utL P40692 MLH1 756 FALSE FALSE FALSE FALSE FALSE FALSE protein homolog 1) DNA polymerase delta catalytic subunit (EC P28340 POLD1 2 .7.7 7) (EC 3.1 . 1.-) (DNA polymerase 1107 FALSE FALSE FALSE TRUE TRUE TRUE subunit delta p125) DNA polymerase delta subunit 2 (DNA P49005 POLD2 469 FALSE FALSE FALSE FALSE TRUE FALSE polymerase delta subunit pSQ) DNA polymerase subunit gamma-1 (EC P54098 POLG 2.7.7.7) (Mitochondrial DNA polymerase 1239 FALSE FALSE TRUE FALSE FALSE FALSE catalytic subunit) (PolG-aipha) DNA repair protein RAD50 (hRADSO) (EC 3.6.- Q92878 RAD5Q 1312 TRUE TRUE FALSE TRUE TRUE FALSE -) DNA replication licensing factor MCM2 (EC P49736 C 2 3.6.4.12) (Minichromosome maintenance 9 4 FALSE FALSE FALSE FALSE FALSE FALSE protein 2 homolog) (Nuclear protein B 28)

DNA replication licensing factor C 3 (EC 3.6.4.12) (DNA polymerase alpha holoenzyme- P25205 C IV 3 808 FALSE FALSE FALSE FALSE FALSE FALSE associated protein P1) (P1- C 3) (RLF subunit beta) (p102)

DNA replication licensing factor C 4 (EC P33991 C 4 863 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.4.12) (CDC21 homolog) (P1-CDC21)

DNA replication licensing factor CM5 (EC P33992 C 5 734 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.4.12) (CDC46 homolog) (P1-CDC46)

DNA replication licensing factor MCM6 (EC Q 14566 CM6 821 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.4.12) (p105MCM)

DNA replication licensing factor CM7 (EC P33993 MCM7 719 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.4.12) (CDC47 homolog) (P1 .1-MCM3)

DNA topoisomerase 1 (EC 5.99.1 .2) (DNA P 1387 TOP1 765 FALSE FALSE FALSE FALSE FALSE FALSE topoisomerase ) DNA topoisomerase 2-a!pha (EC 5.99.1 .3) P 1388 TOP2A 1531 FALSE FALSE FALSE FALSE FALSE FALSE (DNA topoisomerase II, alpha isozyme) DNA topoisomerase 2-beta (EC 5.99.1 .3) QQ2880 TOP2B 1626 FALSE TRUE FALSE FALSE FALSE FALSE (DNA topoisomerase II, beta isozyme) DNA-(apurinic or apyrimidinic site) lyase (EC 3.1-.-) (EC 4.2.99.18) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease P27695 APEX1 318 FALSE FALSE FALSE FALSE FALSE FALSE 1) (AP endonuclease 1) (APE-1) (REF-1) (Redox factor-1) [Cleaved into: DNA-(apurinic or apyrimidinic site) lyase, mitochondrial] DNA-dependent protein kinase catalytic P78527 PRKDC subunit (DNA-PK catalytic subunit) (DNA- 4128 FALSE FALSE FALSE FALSE FALSE FALSE PKcs) (EC 2.7. 11.1) (DNPK1 ) (p460)

DNA-directed RNA polymerase I subunit RPB1 (RNA polymerase I subunit B1) (EC 2.7.7.6) (DNA-directed RNA polymerase P24928 POLR2A 1970 TRUE FALSE FALSE FALSE FALSE FALSE subunit A) (DNA-directed RNA polymerase HI largest subunit) (RNA-directed RNA polymerase subunit RPB1) (EC 2.7.7.48) DNA-directed RNA polymerase subunit RPB2 (EC 2.7.7.6) (DNA-directed RNA polymerase II 140 kDa polypeptide) (DNA- P30876 POLR2B 1174 FALSE FALSE FALSE TRUE TRUE TRUE directed RNA polymerase II subunit B) (RNA polymerase subunit 2) (RNA polymerase subunit B2)

DNA-directed RNA polymerase I subunit RPC1 (RNA polymerase subunit C1) (EC 2.7.7.6) (DNA-directed RNA polymerase III POLR3A largest subunit) (DNA-directed RNA 1390 FALSE FALSE FALSE FALSE FALSE FALSE polymerase III subunit A) (RNA polymerase III 155 kDa subunit) (RPC155) (RNA polymerase III subunit C160) DNA-direcied RNA polymerases I and 111 subunii RPAC1 (DNA-directed RNA polymerase I subunit C) (RNA polymerases I 015160 POLR1C 346 TRUE TRUE FALSE FALSE FALSE FALSE and III subunit AC1) (AC40) (DNA-directed RNA polymerases I and I 40 kDa polypeptide) (RPA40) (RPA39) (RPC40)

DNA-directed RNA polymerases I, II, and III subunit RPABC1 (RNA polymerases I, II, and III subunit ABC1) (DNA-directed RNA P19388 POLR2E 210 FALSE FALSE FALSE FALSE FALSE FALSE polymerase II 23 kDa polypeptide) (DNA- directed RNA polymerase II subunit E) (RPB5 homoiog) (XAP4) DNA-directed RNA polymerases I, II, and III subunit RPABC3 (RNA polymerases I, II, and III subunit ABC3) (DNA-directed RNA P52434 POLR2H polymerase II subunit H) (DNA-directed RNA 150 TRUE TRUE FALSE TRUE TRUE TRUE polymerases I, II, and Hi 17.1 kDa polypeptide) (RPB17) (RPB8 homoiog) (hRPBS)

DnaJ homoiog subfamily A member 1 (DnaJ protein homoiog 2) (HSDJ) (Heat shock 40 P31689 DNAJA1 397 FALSE FALSE FALSE FALSE FALSE FALSE kDa protein 4) (Heat shock protein J2) (HSJ-2) (Human DnaJ protein 2) (hDj-2)

DnaJ homoiog subfamily A member 2 (Cell cycle progression restoration gene 3 protein) 060884 412 FALSE FALSE FALSE TRUE TRUE FALSE (Dnj3) (Dj3) (HIRA-interacting protein 4) (Renal carcinoma antigen NY-REN-14)

DnaJ homoiog subfamily A member 3 , mitochondrial (DnaJ protein Tid-1) (hTid-1) DNAJA3 (Hepatocellular carcinoma-associated antigen 480 FALSE FALSE FALSE FALSE FALSE FALSE 57) (Tumorous imaginai discs protein Tid56 homoiog) DnaJ bomo!og subfamily B member 1 (DnaJ proiein bomo!og 1) (Heat shock 40 kDa P25685 DNAJB1 340 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) (HSP40) (Heat shock protein 40) (Human DnaJ protein 1) (hDj-1)

DnaJ homolog subfamily B member 1 (APOBEC1 -binding protein 2) (ABBP-2) (DnaJ proiein homolog 9) (ER-associated DNAJ) (ER- associated Hsp40 co-chaperone) Q9UBS4 DNAJB1 1 358 FALSE FALSE FALSE TRUE TRUE FALSE (Endoplasmic reticulum DNA J domain- containing protein 3) (ER-resident protein ERdjS) (ERdj3) (ERj3p) (HEDJ) (Human DnaJ protein 9) (hDj-9) (PWP1-interacting protein 4)

DnaJ homolog subfamily C member 10 (EC

- , ...... ,„ . 1.8.4.-) (Endoplasmic reticulum DNA J domain- 38IXB1 DNAJC10n .V . , _ _ . . 793 FALSE FALSE FALSE FALSE FALSE FALSE containing protein 5) (ER-resident protein ERdjS) (ERdj5) (Macrothioredoxin) (MTHr)

9 V H1 DNAJC1 1 DnaJ homolog subfamily C member 11 559 TRUE TRUE FALSE TRUE FALSE FALSE

DnaJ homolog subfamily C member 2 (M- phase phosphoprotein 11) (Zuotin-related 299543 DNAJC2 factor 1) [Cleaved into: DnaJ homolog 621 FALSE FALSE TRUE TRUE TRUE TRUE subfamily C member 2 , N-terminally processed] DnaJ homolog subfamily C member 2 1 (DnaJ 5 F1R6 DNAJC21 homolog subfamily A member 5) (Protein 531 FALSE FALSE FALSE TRUE FALSE FALSE GS3) DnaJ homolog subfamily C member 7 399615 DNAJC7 (Tetratricopeptide repeat protein 2) (TPR 494 TRUE TRUE TRUE FALSE FALSE FALSE repeat protein 2)

075937 DNAJC8 ° n . h ° s b ™ m b 53 FALSE FALSE FALSE FALSE FALSE FALSE (Splicing protein spf31) 2 S b i® b 9 Q8WXX5 DNAJC9 ί , 260 TRUE TRUE FALSE TRUE FALSE FALSE (HDJC9) (DnaJ protein SB73) Dolichol-phosphate mannosyltransferase subunit 1 (EC 2 4.1.83) (Dolichol-phosphate mannose synthase subunit 1) (DPM synthase 060762 DPMI subunit 1) (Dolichyl-phosphate beta-D- 260 FALSE FALSE FALSE FALSE FALSE FALSE mannosyltransferase subunit 1) (Mannose-P- doiichoi synthase subunit 1) (MPD synthase subunit 1) Dolichol-phosphate mannosyltransferase subunit 3 (Dolichol-phosphate mannose synthase subunit 3} (DPM synthase subunit 3) Q9P2X0 DPM3 (Dolichyl-phosphate beta-D- 92 FALSE TRUE FALSE FALSE FALSE FALSE mannosyltransferase subunit 3) (Mannose-P- dolichol synthase subunit 3) (MPD synthase subunit 3) (Prostin-1)

Dolichyl-diphosphooligosaccharide-protein glycosyltransferase 48 kDa subunit (DDOST DDOST 456 TRUE TRUE TRUE TRUE TRUE TRUE 48 kDa subunit) (Oiigosaccharyi transferase 48 kDa subunit)

Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 1 (Dolichyl- P04843 RPN1 diphosphooligosaccharide-protein 607 FALSE FALSE FALSE FALSE FALSE FALSE glycosyltransferase 67 kDa subunit) (Ribophorin ) (RPN-I) (Ribophorin-1)

Dolichyl~diphosphooiigosaccharide--protein glycosyltransferase subunit 2 (Dolichyl- P04844 RPN2 diphosphooligosaccharide-protein 631 FALSE FALSE FALSE TRUE TRUE TRUE glycosyltransferase 63 kDa subunit) (RIBIIR) (Ribophorin II) (RPN-II) (Ribophorin-2)

Dolichyl-diphosphooligosaccharide-protein

P61803 DAD1 subunit DAD1 113 FALSE FALSE FALSE TRUE FALSE FALSE (Oiigosaccharyi transferase subunit DAD1) (Defender against cell death 1) (DAD-1) Dolichyl~diphosphoo!igosaccharide-~protein glycosyltransferase subunit STT3A (Oligosaccharyi transferase subunit STT3A) P46977 STT3A 7Q5 FALSE FALSE FALSE FALSE FALSE FALSE (STT3-A) (EC 2.4.99.18) (B5) (Integra! membrane protein 1) (Transmembrane protein TMC) Dolichyl-diphosphoo!igosaccharide-protein glycosyltransferase subunit STT3B (Oligosaccharyi transferase subunit STT3B) Q8TCJ2 STT3B 826 FALSE TRUE TRUE FALSE FALSE FALSE (STT3-B) (EC 2.4.99. 8) (Source of immunodominant MHC-associated peptides homolog) Double-stranded RNA-binding protein Sfaufen 095793 STAU1 577 FALSE FALSE FALSE FALSE FALSE FALSE homolog 1 Double-stranded RNA-specific adenosine deaminase (DRADA) (EC 3.5.4.37) (136 kDa Ρ55265 ADAR double-stranded RNA-binding protein) (p136) 1226 FALSE FALSE FALSE ∆ S FALSE (Interferon-inducible protein 4) (!F!-4) (K88DSRBP) P59S94 DCDC1 Doublecortin domain-containing protein 1 354 FALSE FALSE FALSE FALSE FALSE FALSE Drebrin (Developmenta!iy-reguiated brain Q 16643 DBN1 649 FALSE F F . 3 E TRUE TRUE TRUE protein)

Drebrin-like protein (Cervical SH3P7) (Cervical mucin-associated protein) (Drebrin-F) (HPK1- Q9UJU6 DBNL 430 FALSE FALSE FALSE FALSE FALSE FALSE interacting protein of 55 kDa) (HIP-55) (SH3 domain-containing protein 7)

Dual specificity mitogert-activated protein kinase kinase 1 (MAP kinase kinase 1) Q02750 ΜΑΡ2 Κ1 (MAPKK 1) (MKK1) (EC 2.7.12.2) (ERK 393 FALSE TRUE FALSE FALSE TRUE FALSE activator kinase 1) (MAPK/ERK kinase 1) (MEK 1) Dual specificity mitogert-activated protein kinase kinase 2 (MAP kinase kinase 2) Ρ36507 ΜΑΡ2 Κ2 400 FALSE FALSE FALSE FALSE TRUE TRUE (MAPKK 2) (EC 2.7.12.2) (ERK activator kinase 2) (MAPK/ERK kinase 2) (MEK 2) Dynactin subunit 1 (150 kDa dynein- Q14203 DCTN1 associated polypeptide) (DAP-1 50) (DP-1 50) 1278 FALSE FALSE FALSE FALSE FALSE FALSE (p135) (p150-g!ued) Dynactin subunit 2 (50 kDa dynein-associated Q13561 DCTN2 polypeptide) (Dynactin complex 50 kDa FALSE FALSE FALSE FALSE FALSE FALSE subunit) (DCTN-50) (p50 dynamitin)

Dynamin-1-like protein (EC 3.6.5 5) (Dnm1p/Vps1p-like protein) (DVLP) (Dynamin family member proline-rich carboxyi-terminal 1 736 FALSE FALSE FALSE FALSE FALSE FALSE domain less) (Dymple) (Dynamin-like protein) (Dynamin-like protein 4) (Dynamin-like protein IV) (HdynlV) (Dynamin-related protein 1)

P50570 DN Dynamin-2 (EC 3.6.5.5) 870 FALSE TRUE TRUE TRUE TRUE FALSE Dynamin-like 120 kDa protein, mitochondrial (EC 3.6.5.5) (Optic atrophy protein 1) 060313 OPA1 960 FALSE TRUE FALSE! FALSE. FALSE FALSE [Cleaved into: Dynamin-like 120 kDa protein, form S1] Dynein heavy chain 8 , axonemal (Axonemai Q96JB1 DNAH8 beta dynein heavy chain 8) (Ciliary dynein 4490 FALSE FALSE FALSE FALSE FALSE FALSE heavy chain 8) Dynein light chain 1, cytoplasmic (8 kDa dynein light chain) (DLC8) (Dynein light chain P63167 DYNLL1 89 FALSE FALSE FALSE FALSE FALSE FALSE LC8-type 1) (Protein inhibitor of neuronal nitric oxide synthase) (PIN) Dynein light chain Tctex-type 1 (Protein CW-1) P63172 DYNLT1 113 FALSE FALSE FALSE FALSE FALSE FALSE (T-compiex testis-specific protein 1 homolog)

E3 SUMO-protein iigase RanBP2 (EC 6.3.2.-) (358 kDa nucleoporin) (Nuclear pore complex 3224 FALSE TRUE FALSE! FALSE FALSE FALSE protein Nup358) (Nucleoporin Nup358) (Ran- binding protein 2) (RanBP2) (p270) E3 ubiquitin-protein ligase ARIH2 (ARI-2) (Protein ariadne-2 homolog) (EC 2 3.2.-) 095376 ARIH2 493 TRUE FALSE FALSE FALSE FALSE FALSE (RING-type E3 ubiquitin transferase ARIH2) (Triad 1 protein)

E3 ubiquitin-protein iigase HUWE1 (EC 2.3.2.26) (ARF-binding protein 1) (ARF-BP1) (HECT, UBA and VW E domain-containing protein 1) (HECT-type E3 ubiquitin transferase HUWE1) (Homologous to E6AP carboxyi Q7Z6Z7 HUWE1 4374 FALSE FALSE FALSE FALSE FALSE FALSE terminus homologous protein 9) (HectH9) (Large structure of UREB1) (LASU1) (Mcl-1 ubiquitin ligase E3) (Mule) (Upstream regulatory element-binding protein 1) (URE- B1) (URE-binding protein 1)

E3 ubiquitin-protein ligase KCMF1 (EC 2.3.2.27) (FGF-induced in gastric cancer) (Potassium channel modulatory factor) Q9P0J7 KC F1 381 FALSE FALSE FALSE FALSE FALSE FALSE (PCMF) (R G-type E3 ubiquitin transferase KCMF1) (ZZ-type zinc finger-containing protein 1)

E3 ubiquitin-protein ligase RNF1 14 (EC 2.3.2.27) (RING finger protein 114) (RING- Q9Y508 RNF1 14 228 FALSE FALSE FALSE FALSE FALSE FALSE type E3 ubiquitin transferase RNF1 14) (Zinc finger protein 228) (Zinc finger protein 313)

E3 ubiquitin-protein ligase TRIM56 (EC 2.3.2.27) (RING finger protein 109) (RING- Q9BRZ2 TR 56 755 FALSE FALSE FALSE FALSE FALSE FALSE type E3 ubiquitin transferase TRIM56) (Tripartite motif-containing protein 56) E3 ubiquitin-protein ligase UBR4 (EC 2.3.2.27) (600 kDa retinoblastoma protein-associated factor) (N-recognin-4) (RING-type E3 ubiquitin Q5T4S7 UBR4 5183 FALSE FALSE FALSE FALSE FALSE FALSE transferase UBR4) (Retinoblastoma- associated factor of 600 kDa) (RBAF600) (p600) (Zinc finger UBR1-type protein 1)

E3 ubiquitin-protein ligase UBR5 (EC 2.3.2 26) (E3 ubiquitin-protein ligase, HECT domain- 095071 UBR5 containing 1) (HECT-type E3 ubiquitin 2799 FALSE FALSE FALSE TRUE FALSE FALSE transferase UBR5) (Hyperplastic discs protein homoiog) (hHYD) (Progestin-induced protein)

E3 ubiquitin/ISG15 ligase TR 25 (EC 6.3.2.n3) (Estrogen-responsive finger protein) (RING finger protein 147) (RING-type E3 ubiquitin transferase) (EC 2.3.2.27) (RING- Q14258 TR 25 630 FALSE FALSE FALSE TRUE FALSE TRUE type E3 ubiquitin transferase TRIM25) (Tripartite motif-containing protein 25) (Ubiquitin/ISG15-conjugating enzyme TRIM25) (Zinc finger protein 147)

E3 UFM1-protein ligase 1 (EC 6.3.2.-) (Novel 094874 UFL1 LZAP-binding protein) (Regulator of 794 FALSE FALSE FALSE FALSE FALSE FALSE C53/LZAP and DDRGK1) elF-2-aipha kinase activator GCN1 (GCN1 elF- 2-alpha kinase activator homoiog) (GCN1~like Q92616 GCN1 protein 1) (General control of amino-acid 2671 FALSE FALSE FALSE TRUE TRUE FALSE synthesis 1-like protein 1) (Translational activator GCN1) (HsGCNI)

EKC/KEOPS complex subunit TPRKB (PRPK- Q9Y3C4 TPRKB 175 FALSE FALSE FALSE FALSE FALSE FALSE binding protein) (TP53RK-binding protein)

015717 ELAVL1 ELAV-like protein 1 (Hu-antigen R) (HuR) 326 FALSE FALSE FALSE FALSE FALSE FALSE Electron transfer fiavoprotein subunit alpha, P13804 ETFA 333 FALSE FALSE FALSE FALSE FALSE FALSE mitochondrial (Alpha-ETF) Electron transfer flavoprotein subunit beta P381 7 ETFB 255 FALSE FALSE FALSE FALSE FALSE FALSE (Beta-ETF) Electron transfer fiavoprotein-ubiquinone oxidoreductase, mitochondrial (ETF-QO) (ETF- Q16134 ETFDH ubiquinone oxidoreductase) (EC 1 5.5.1) 617 FALSE FALSE FALSE FALSE FALSE FALSE (Electron-transferring-flavoprotein dehydrogenase) (ETF dehydrogenase) Elongation factor 1-alpha 1 (EF~1~alpha-1) (Elongation factor Tu) (EF-Tu) (Eukaryotic P68104 EEF1A1 462 FALSE FALSE FALSE FALSE FALSE FALSE elongation factor 1 A-1) (eEF1A-1) (Leukocyte receptor duster member 7) P24534 EEF1 B2 Elongation factor 1-beta (EF-1-beta) 225 FALSE FALSE FALSE FALSE FALSE FALSE Elongation factor 1-delta (EF-1 -delta) (Antigen P29692 EEF1 D 281 FALSE FALSE FALSE FALSE FALSE FALSE NY-CO-4) Elongation factor 1-gamma (EF-1 -gamma) P26641 EEF1G 437 FALSE FALSE FALSE FALSE FALSE FALSE (eEF-1 B gamma) P13639 EEF2 Elongation factor 2 (EF-2) 858 FALSE FALSE TRUE FALSE FALSE FALSE

Elongation factor G , mitochondrial (EF-Gmt) GF 1 (Elongation factor G 1, mitochondrial) (mEF-G 751 TRUE FALSE FALSE TRUE FALSE TRUE 1) (Elongation factor G1) (hEFG1)

Elongation factor Ts, mitochondrial (EF-Ts) P43897 TSF 325 FALSE TRUE FALSE FALSE FALSE FALSE (EF-TsMt) Elongation factor Tu, mitochondrial (EF-Tu) P4941 1 TUF 452 FALSE FALSE FALSE FALSE FALSE FALSE (P43) Elongation factor-like GTPase 1 (Elongation factor Tu GTP-binding domain-containing Q7Z2Z2 EFL1 1120 FALSE FALSE FALSE TRUE FALSE FALSE protein 1) (Elongation factor-like 1) (Protein FAM42A) Elongator complex protein 1 (ELP1) (IkappaB 095163 IKBKAP kinase complex-associated protein) (IKK 1332 FALSE FALSE FALSE FALSE FALSE FALSE complex-associated protein) (p150)

Elongator complex protein 3 (hELP3) (EC Q9H9T3 ELP3 547 FALSE FALSE FALSE FALSE FALSE FALSE 2.3.1 .48) Elongator complex protein 4 (hELP4) (PAX8 Q96EB1 ELP4 424 FALSE FALSE FALSE FALSE FALSE FALSE neighbor gene protein) P50402 EMD Emerin 254 FALSE FALSE FALSE TRUE TRUE TRUE Endophilin-B1 (Bax-interacting factor 1) (Bif-1) Q9Y371 SH3GLB1 (SH3 domain-containing GRB2-like protein 365 FALSE FALSE FALSE FALSE FALSE FALSE B1) Endophilin-B2 (SH3 domain-containing GRB2- 395 FALSE FALSE FALSE FALSE FALSE FALSE l ke protein B2)

Endoplasmic reticulum aminopeptidase 1 (EC 3.4.1 1.-) (ARTS-1) (Adipocyte-derived leucine aminopeptidase) (A-LAP) (Aminopeptidase Q9NZ08 ERAP1 PiLS) (Puromycin-insensitive leucyl-specific 941 TRUE FALSE FALSE FALSE FALSE FALSE aminopeptidase) (PILS-AP) (Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator)

Endoplasmic reticulum resident protein 29 (ERp29) (Endoplasmic reticulum resident Ρ30040 ERP29 261 FALSE FALSE! FALSE FALSE FALSE -4 protein 28) (ERp28) (Endoplasmic reticulum resident protein 31) (ERp31) Endoplasmic reticulum resideni protein 44 (ER Q9BS26 ERP44 protein 44) (ERp44) (Thioredoxin domain- 406 FALSE FALSE FALSE TRUE TRUE FALSE containing protein 4) Endoplasmin (94 kDa glucose-regulated protein) (GRP-94) (Heat shock protein 90 kDa P14625 HSP90B1 803 FALSE FALSE FALSE FALSE FALSE FALSE beta member 1) (Tumor rejection antigen 1) (gp96 homoiog)

Enhancer of mRNA-decapping protein 3 (LSM16 homoiog) (YjeF N-terminal domain- Q96F86 EDC3 508 FALSE FALSE FALSE FALSE FALSE FALSE containing protein 2) (YjeF__N2) (hYjeF_N2) (YjeF domain-containing protein 1)

Enhancer of mRNA-decapping protein 4 (Autoantigen Ge-1) (Autoantigen RCD-8) Q6P2E9 EDC4 1401 FALSE FALSE FALSE FALSE FALSE FALSE (Human enhancer of decapping large subunit) (Hedls) P84090 ERH Enhancer of rudimentary homo!og 104 FALSE FALSE FALSE FALSE FALSE FALSE

Enoyl-CoA delta isomerase 2 , mitochondrial (EC 5.3 3.8) (DRS-1) (Delta(3),delta(2)-enoyl- CoA isomerase) (D3,D2-enoyl-CoA isomerase) (Diazepam-binding inhibitor- 075521 ECI2 related protein 1) (DBI-related protein 1) 394 FALSE TRUE FALSE FALSE FALSE FALSE (Dodecenoyl-CoA isomerase) (Hepatocellular carcinoma-associated antigen 88) (Peroxisomal 3,2-trans-enoyl-CoA isomerase) (pECI) (Renal carcinoma antigen NY-REN-1)

Enoyl-CoA hydratase, mitochondrial (EC ECHS1 4.2.1 .17) (Enoyl-CoA hydratase 1) (Short- 290 FALSE FALSE FALSE TRUE TRUE TRUE chain enoyl-CoA hydratase) (SCEH) Equilibrative nucleoside transporter 1 (Equilibrative nitrobenzyimercaptopurine riboside-sensitive nucleoside transporter) Q99808 SLC29A1 456 TRUE TRUE FALSE FALSE FALSE TRUE (Equilibrative NBMPR-sensitive nucleoside transporter) (Nucleoside transporter, es-type) (Solute carrier family 29 member 1)

Q8N766 EMC1 ER membrane protein complex subunit 1 993 TRUE TRUE FALSE TRUE TRUE TRUE ER membrane protein complex subunit 8 043402 E C8 210 FALSE FALSE FALSE FALSE FALSE FALSE (Neighbor of COX4) (Protein FAM158B) Erlin-1 (Endoplasmic reticulum lipid raft- associated protein 1) (Protein KE04) 075477 ERLIN1 (Stomatin-prohibitin-flotillin-HflC/K domain- 346 FALSE FALSE FALSE TRUE TRUE FALSE containing protein 1) (SPFH domain- containing protein 1) EROI-like protein alpha (ERQ1-L) (ER01-L- alpha) (EC 1.8.4.-) (Endoplasmic Q96HE7 ERQ1A oxidoreductin-1-like protein) (Endoplasmic 468 FALSE FALSE FALSE FALSE FALSE FALSE reticulum oxidoreductase alpha) (Oxidoreductin-1-L-alpha) ES1 protein homolog, mitochondrial (Protein 2 C21orf33 268 FALSE FALSE FALSE TRUE FALSE FALSE GT335) (Protein KNP-I) Estradiol 17-beta-dehydrogenase 1 (EC 1. 1 . 1 .62) ( 17-beia-hydroxysteroid dehydrogenase 11) (17-beta-HSD 11) (17bHSD1 1) (17betaHSD1 1) (17-beta- hydroxysteroid dehydrogenase XI) (17-beta- HSD XI) (17betaHSDXI) (Cutaneous T-cell HSD17B1 Q8NBQ5 lymphoma-associated antigen HD-CL-03) 300 TRUE TRUE TRUE FALSE TRUE TRUE (CTCL-associated antigen HD-CL-03) (Dehydrogenase/reductase SDR family member 8) (Retina! short-chain dehydrogenase/reduciase 2) (retSDR2) (Short chain dehydrogenase/reductase family 16C member 2) Eukaryotic initiation factor 4A-I (elF-4A-l) P60842 EIF4A1 (elF4A-l) (EC 3.6.4.13) (ATP-dependent RNA 406 FALSE FALSE FALSE TRUE TRUE TRUE helicase elF4A-1) Eukaryotic initiation factor 4A-II (elF-4A-ll) Q14240 EIF4A2 (elF4A-ll) (EC 3.6.4.13) (ATP-dependent RNA 407 TRUE FALSE TRUE TRUE FALSE TRUE helicase elF4A~2) Eukaryotic initiation factor 4A-III (elF-4A-lii) (elF4A-lll) (EC 3.6.4.13) (ATP-dependent RNA helicase DDX48) (ATP-dependent RNA helicase elF4A-3) (DEAD box protein 48) P38919 EIF4A3 (Eukaryotic initiation factor 4A-like NUK-34) 4 11 FALSE FALSE FALSE FALSE FALSE FALSE (Eukaryotic translation initiation factor 4A isoform 3) (Nuclear matrix protein 265) (N P 265) (hNMP 265) [Cleaved into: Eukaryotic initiation factor 4 .- Ill, N-terminally processed]

Eukaryotic peptide chain release factor GTP- binding subunit ERF3A (Eukaryotic peptide 499 FALSE FALSE FALSE TRUE TRUE FALSE chain release factor subunit 3a) (eRF3a) (G1 to S phase transition protein 1 homoiog) Eukaryotic peptide chain release factor P62495 ETF1 subunit 1 (Eukaryoiic release factor 1) (eRF1) 437 TRUE TRUE TRUE FALSE TRUE TRUE (Protein CM) (TB3-1) Eukaryotic translation elongation factor 1 epsilon-1 (Aminoacyl iRNA synthetase 043324 EEF1E1 complex-interacting multifunctional protein 3) 174 TRUE TRUE FALSE FALSE FALSE FALSE (Elongation factor p18) (Multisynthase complex auxiliary component p18) Eukaryotic translation initiation factor 1b 060739 EIF1B (elF1b) (Protein translation factor SUM 113 TRUE FALSE FALSE FALSE FALSE FALSE homolog GC2Q) Eukaryotic translation initiation factor 2 subunit 1 (Eukaryoiic translation initiation factor 2 P05198 EIF2S1 3 FALSE! FALSE! FALSE! FALSE FALSE! FALSE subunit alpha) (elF-2-alpha) (elF-2A) (elF- 2alpha) Eukaryotic translation initiation factor 2 subunit P20042 EIF2S2 2 (Eukaryotic translation initiation factor 2 333 FALSE FALSE FALSE FALSE FALSE FALSE subunit beta) (elF-2-beta) Eukaryotic translation initiation factor 2 subunit P41091 EIF2S3 3 (Eukaryotic translation initiation factor 2 472 FALSE FALSE FALSE FALSE FALSE FALSE subunit gamma X) (elF-2-gamma X) (elF-2gX)

Eukaryotic translation initiation factor 2A (elF- 2A) (65 kDa eukaryotic translation initiation Q9BY44 E F2A 585 FALSE FALSE FALSE FALSE FALSE FALSE factor 2A) [Cleaved into: Eukaryotic translation initiation factor 2A, N-terminaliy processed] Eukaryotic translation initiation factor 2D P41214 EIF2D (elF2d) (Hepatocellular carcinoma-associated 584 FALSE FALSE FALSE FALSE TRUE TRUE antigen 56) (Ligatin) Eukaryoiic translation initiation factor 3 subunit A (elF3a) (Eukaryotic translation initiation Q14152 EIF3A 1382 TRUE TRUE TRUE TRUE TRUE TRUE factor 3 subunit 1 ) (elF-3-theta) (eiF3 p167) (elF3 p180) (elF3 p185) Eukaryotic translation initiation factor 3 subunit B (elF3b) (Eukaryotic translation initiation P55884 EIF3B 814 FALSE FALSE FALSE FALSE FALSE FALSE factor subunit 9) (Prt1 homolog) (hPrtl) (elF- 3-eta) (elF3 p 110) (elF3 p 116) Eukaryotic translation initiation factor 3 subunit Q99613 EIF3C C (e!F3c) (Eukaryotic translation initiation FALSE FALSE FALSE FALSE FALSE FALSE factor subunit 8) (elF3 p 110) Eukaryotic translation initiation factor 3 subunit 015371 EIF3D D (elF3d) (Eukaryoiic translation initiation 548 F L3 Ε A L Ξ F L3 Ε F LS Ε FA LS E FA factor 3 subunit 7) (elF-3-zeta) (elF3 p66)

Eukaryotic translation initiation factor 3 subunit E (elF3e) (Eukaryotic translation initiation P60228 EIF3E FALSE TRUE FALSE TRUE TRUE TRUE factor 3 subunit 6) (Viral integration site protein INT-6 homolog) (elF-3 p48)

Eukaryoiic translation initiation factor 3 subunit F (elF3f) (Deubiquitinating enzyme elF3f) (EC 000303 EIF3F 357 TRUE FALSE FALSE FALSE FALSE FALSE 3.4.19 12) (Eukaryotic translation initiation factor s subunit 5) (elF-3-epsilon) (elF3 p47)

Eukaryotic translation initiation factor 3 subunit G (elF3g) (Eukaryotic translation initiation factor 3 RNA-binding subunit) (elF-3 RNA- 075821 E1F3G 320 FALSE FALSE FALSE FALSE FALSE FALSE binding subunit) (Eukaryotic translation initiation factor 3 subunit 4) (e!F-3-de!ta) (e F3 p42) (e F3 p44) Eukaryotic translation initiation factor 3 subunit H (elF3h) (Eukaryotic translation initiation 015372 EIF3H 352 FALSE FALSE FALSE FALSE FALSE FALSE factor 3 subunit 3) (e!F-3-gamma) (e!F3 p40 subunit)

Eukaryotic translation initiation factor 3 subunit ( e F3i) (Eukaryotic translation initiation factor Q13347 EIF3I 325 FALSE FALSE FALSE FALSE FALSE FALSE 3 subunit 2) (TGF-beta receptor-interacting protein 1) (TRIP-1) (elF-3-beta) (e!F3 p36) Eukaryotic translation initiation factor 3 subunit 075822 E F3J J (e! F3j) (Eukaryotic translation initiation factor 58 FALSE FALSE FALSE FALSE FALSE FALSE 3 subunit 1) (e F-3-alpha) (e F3 p35)

Eukaryotic translation initiation factor 3 subunit K (e F3k) (Eukaryotic translation initiation Q9UBQ5 E IF3K FALSE FALSE TRUE FALSE FALSE FAL factor 3 subunit 2) (Muscle-specific gene 9 protein) (PLAC-24) (el F-3 p25) (e F-3 p28)

Eukaryotic translation initiation factor 3 subunit L (e F ) (Eukaryotic translation initiation factor Q9Y262 E IF3L 3 subunit 6-interacting protein) (Eukaryotic 564 FALSE FALSE FALSE FALSE FALSE FALSE translation initiation factor 3 subunit E- inferacting protein)

Eukaryotic translation initiation factor 3 subunit Q7L2H7 E F3 (el F3m) (Fetal lung protein B5) (hFL-B5) 374 FALSE FALSE FALSE TRU E FALSE TRUE (PCI domain-containing protein 1)

Eukaryotic translation initiation factor 4 QQ4637 E F4G 1 gamma 1 (el F~4~gamma 1) (el F-4G 1) (e F- 1599 FALSE FALSE FALSE FALSE FALSE FALSE 4G 1) (p220)

Eukaryotic translation initiation factor 4 P78344 E F4G2 gamma 2 (e! F-4-gamma 2) (el F-4G 2) (el F4G 907 FALSE FALSE FALSE FALSE FALSE FALSE 2) (Death-associated protein 5) (DAP-5) (p97)

Eukaryotic translation initiation factor 4B (el F- P23588 E IF4B 6 11 FALSE FALSE FALSE FALSE FALSE FALSE 4B) Eukaryotic translation initiation factor 4E (el F- P06730 E IF4E 4E) (el F4E) (el F-4F 25 kDa subunit) (mRNA 2 17 FALSE FALSE FALSE FALSE FALSE FALSE cap-binding protein) Eukaryotic translation initiation factor 4H (el F- Q 5056 E IF4H 4H) (Williams-Beuren syndrome chromosomal 248 FALSE FALSE FALSE FALSE FALSE FALSE region 1 protein)

P5501 0 E F5 Eukaryotic translation initiation factor 5 (el F-5) 431 FALSE FALSE FALSE FALSE TRUE FALSE Eukaryotic translation initiation factor 5A~1 (elF-5A-1) (elF-5A1) (Eukaryotic initiation P63241 EIF5A 154 FALSE FALSE FALSE FALSE FALSE FALSE factor 5A isoform 1) (elF-5A) (Rev-binding factor) (e!F-4D) Eukaryotic translation initiation factor 5B (elF- 060841 EIF5B 5B) (EC 3 6.5.3} (Translation initiation factor 1220 FALSE FALSE FALSE TRUE FALSE FALSE IF-2) Eukaryotic translation initiation factor 6 (elF-6) P56537 E F6 (B(2)GCN homolog) (B4 integrin interactor) 245 FALSE FALSE FALSE FALSE FALSE FALSE (CAB) (p27(BBP)) Exocyst complex component 1 (Exocyst Q9NV70 EXOC1 894 FALSE FALSE! FALSE FALSE! FA L complex component Sec3) Exocyst complex component 4 (Exocyst Q96A65 EXOC4 974 FALSE FALSE TRUE FALSE FALSE FA LS complex component Sec8) Exosome complex component CSL4 Q9Y3B2 EXOSC1 195 FALSE F LS E FALSE! FALSE FALSE FALSE (Exosome component 1) Exosome complex component RRP4 Q 13868 EXOSC2 (Exosome component 2) (Ribosomal RNA- 293 FALSE FALSE FALSE FALSE FALSE FALSE processing protein 4) Exosome complex component RRP40 Q9NQT5 EXOSC3 (Exosome component 3) (Ribosomal RNA- 275 TRUE FALSE FALSE TRUE TRUE FALSE processing protein 40) (p10)

Exosome component 1 (EC 3.1 .13.-) (Autoantigen PM/Scl 2) (P100 polymyositis- scleroderma overlap syndrome-associated Q01780 885 TRUE FALSE FALSE FALSE FALSE FALSE autoantigen) (Polymyositis/scleroderma autoantigen 100 kDa) (PM/Scl-100) (Polymyositis/scleroderma autoantigen 2)

Exportin-1 (Exp1) (Chromosome region 014980 XP01 1071 FALSE FALSE FALSE TRUE TRUE TRUE maintenance 1 protein homolog) Exportin-2 (Exp2) (Cellular apoptosis susceptibility protein) (Chromosome P55060 0 3 L 971 FALSE FALSE FALSE FALSE FALSE FALSE segregation 1-like protein) ( mpor in-a pha re- exporter) Q9HAV4 XP05 Exportin-5 (Exp5) (Ran-binding protein 21) 1204 FALSE FALSE FALSE FALSE FALSE FALSE Q9UIA9 XP07 Exportin-7 (Exp7) (Ran-binding protein 16) 1087 TRUE TRUE FALSE TRUE FALSE FALSE 043592 XPOT Exportin-T (Exportin(tRNA)) (tRNA exportin) 962 FALSE FALSE FALSE TRUE TRUE FALSE Extended synaptotagmin-1 (E-Syt1) Q9BSJ8 ESYT1 (Membrane-bound C2 domain-containing 1104 FALSE FALSE FALSE TRUE TRUE TRUE protein)

A0FGR8 ESYT2 Extended synaptotagmin-2 (E-Syt2) (Chr2Syt) 921 TRUE FALSE TRUE FALSE FALSE FALSE

P1531 1 EZR Ezrin (Cytoviiiin) (Villin-2) (p81) 586 FALSE FALSE FALSE FALSE FALSE FALSE F-actin-capping protein subunit alpha- 1 (CapZ P52907 CAPZA1 286 FALSE FALSE FALSE FALSE FALSE FALSE alpha-1) F-actin-capping protein subunit aipha-2 (CapZ P47755 CAPZA2 286 FALSE FALSE FALSE FALSE FALSE FALSE alpha-2) F-actin-capping protein subunit beta (CapZ P47756 277 FALSE FALSE FALSE FALSE FALSE FALSE beta) F-box-like/WD repeat-containing protein TBL1XR1 (Nuclear receptor Q9BZK7 TBL1XR1 corepressor/HDACS complex subunit TBLR1 ) 514 FALSE FALSE FALSE TRUE TRUE FALSE (TBL1 -related protein 1) (Transducin beta-like 1X~reiated protein 1) FACT complex subunit SPT16 (Chromatin- specific transcription elongation factor 140 kDa subunit) (FACT 140 kDa subunit) Q9Y5B9 SUPT16H 1047 FALSE FALSE FALSE FALSE FALSE FALSE (FACTp140) (Facilitates chromatin transcription complex subunit SPT16) (hSPT16)

FACT complex subunit SSRP1 (Chromatin- specific transcription elongation factor 80 kDa subunit) (Facilitates chromatin transcription complex 80 kDa subunit) (FACT 80 kDa Q08945 SSRP1 subunit) (FACTpSO) (Facilitates chromatin 709 FALSE FALSE FALSE FALSE FALSE FALSE transcription complex subunit SSRP1) (Recombination signal sequence recognition protein 1) (Structure-specific recognition protein 1) (hSSRPI) (T160) Fanconi anemia group D2 protein (Protein Q9BXW9 FANCD2 5 1 FALSE FALSE FALSE FALSE TRUE FALSE FACD2) Far upstream element-binding protein 1 (FBP) Q96AE4 FUBP1 (FUSE-binding protein 1) (DNA he!icase V) 44 FALSE FALSE FALSE FALSE FALSE FALSE (hDH V) Far upstream element-binding protein 2 Q92945 KHSRP (FUSE-binding protein 2) (KH type-splicing 7 11 FALSE FALSE FALSE FALSE FALSE FALSE regulatory protein) (KSRP) (p75) Far upstream element-binding protein 3 Q96I24 FUBP3 572 FALSE FALSE FALSE TRUE TRUE TRUE (FUSE-binding protein 3) Famesyl pyrophosphate synthase (FPP synthase) (FPS) (EC 2.5.1 .10) ((2E.6E)- farnesyl diphosphate synthase) FDPS FALSE FALSE FALSE FALSE FALSE FALSE (Dimethylallyltranstransferase) (EC 2.5.1.1) 9 (Famesyl diphosphate synthase) (Geranyltranstransferase) FAS-associated factor 1 (hFAF1) (UBX Q9UNN5 FAF1 domain-containing protein 12) (UBX domain- 650 FALSE FALSE FALSE FALSE FALSE FALSE containing protein 3A) FAS-associated factor 2 (Protein ETEA) (UBX Q96CS3 FAF2 domain-containing protein 3B) (UBX domain- FALSE FALSE FALSE TRUE TRUE TRUE containing protein 8) Fascin (55 kDa actin-bundling protein) (Singed- Q16658 FSCN1 FALSE FALSE FALSE FALSE FALSE FALSE ike protein) (p55) FAST kinase domain-containing protein 2 , Q9NYY8 FASTKD2 FALSE FALSE FALSE FALSE FALSE FALSE mitochondrial Fatty acid synthase (EC 2.3.1 .85) [Includes: [Acyl-carrier-protein] S-acetyltransferase (EC 2.3.1 .38); [Acyl-carrier-protein] S- malonyltransferase (EC 2.3.1 .39); 3-oxoacyl- [acyl-carrier-protein] synthase (EC 2.3.1 .41); 3- 251 1 FALSE FALSE FALSE FALSE FALSE FALSE oxoacyl-[acyl-carrier-protein] reductase (EC . 1 . .100); 3-hydroxyacyl-[acyl-carrier-protein] dehydratase (EC 4.2.1 .59); Enoyl-[acyl-carrier- protein] reductase (EC 1.3.1 .39); Oleoyl-[acyl- carrier- protein] hydrolase (EC 3.1 .2.14)]

Fermitin family homoiog 3 (Kindlin-3) ( IG2- Q86UX7 FER T3 667 FALSE FALSE FALSE FALSE FALSE FALSE ike protein) (Unc-1 12-related protein 2)

Ferrochelatase, mitochondrial (EC 4.99.1 .1) P22830 FECH 423 FALSE FALSE FALSE TRUE TRUE TRUE (Heme synthase) (Protoheme ferro-lyase)

Fiiamin-A (FLN-A) (Actin-binding protein 280) (ABP-280) (Aipha-fi!amin) (Endothelial actin- P21333 FLNA 2647 FALSE FALSE FALSE! FALSE. FALSE FALSE binding protein) (Filamin-1) (Non-muscle filamin)

Filamin-B (FLN-B) (ABP-278) (ABP-280 homo!og) (Actin-binding-like protein) (Beta- 075369 FLNB filamin) (Filamin homoiog 1) (Fh1) (Filamin-3) 2602 FALSE FALSE FALSE FALSE FALSE FALSE (Thyroid autoantigen) (Truncated actin-binding protein) (Truncated ABP)

FK506-binding protein 5 (FKBP-15) (133 kD FK506-binding protein) (133 kDa FKBP) Q5T 1 5 FKBP15 1219 FALSE FALSE FALSE FALSE FALSE TRUE (FKBP-133) (WASP- and FKBP-like protein) (WAFL) Flap endonuclease 1 (FEN-1 ) (EC 3 .1.-.-) (DNase IV) (Flap structure-specific FEN1 380 FALSE FALSE FALSE FALSE FALSE endonuclease 1) (Maturation factor 1) (MF1) (hFEN-1) -v Fragile menial retardation syndrome-related r 4 rXKI , . . , ,-. 621 FALSE FALSE FALSE TRUE FALSE TRUE protein 1 (hFXRIp)™ - Fragile X mental retardation syndrome-related 673 FALSE FALSE FALSE FALSE FALSE FALSE protein 2 Fructose-bisphosphate aldolase A (EC P04075 ALDOA 4.1 .2 13) (Lung cancer antigen NY-LU-1) 364 FALSE FALSE FALSE FALSE FALSE FALSE (Muscle-type aldolase) P09972 ALDOC Fructose-bisphosphate aldolase C (EC 364 FALSE FALSE FALSE FALSE FALSE FALSE 4.1 .2.13) (Brain-type aldolase) p Fumarate hydratase, mitochondrial 510 TRUE TRUE FALSE FALSE FALSE FALSE (Fumarase) (EC 4.2.1 .2) G patch domain and OW motifs-containing Q92917 GPKOW protein (G patch domain-containing protein 5) 476 FALSE FALSE FALSE FALSE FALSE FALSE (Protein OS2 homolog) (Protein T54) GPATCH Q5T3I0 G patch domain-containing protein 4 446 TRUE FALSE FALSE FALSE FALSE FALSE Q12849 GRSF1 G-rich sequence factor 1 (GRSF-1) 480 FALSE FALSE FALSE FALSE FALSE FALSE -4 P51570 GALK1 Galactokinase (EC 2.7.1 .6) (Galactose kinase) 3 2 F S ! F E F L F L FAL FALSE

Gamma-soluble NSF attachment protein Q99747 (SNAP-gamma) (N-efhylmaleimide-sensitive 312 TRUE FALSE FALSE FALSE FALSE FALSE factor attachment protein gamma)

Gamma-tubulin complex component 3 (GCP- TUBGCP 3) (hGCP3) (Gamma-ring complex protein 104 Q96CW5 907 FALSE FALSE FALSE FALSE FALSE FALSE 3 kDa) ( 04p) (hGrip104) (Spindle pole body protein Spc98 homolog) (hSpc98) Q8TEQ6 GEMINS Gem-associated protein 5 (GeminS) 1508 FALSE FALSE FALSE FALSE FALSE FALSE

General transcription factor 3C polypeptide 1 (TF3C-alpha) (T F C box B-binding subunit) Q12789 GTF3C1 (Transcription factor IMC 220 kDa subunit) 2109 FALSE FALSE FALSE FALSE FALSE TRUE (TFIilC 220 kDa subunit) (TFIIIC220) (Transcription factor N C subunit alpha) General transcription factor 3C polypeptide 3 (Transcription factor MIC 102 kDa subunit) Q9Y5Q9 GTF3C3 (TFIIIC 102 kDa subunit) (TFIIIC1 02) 886 FALSE FALSE FALSE TRUE TRUE TRUE (Transcription factor C subunit gamma) (TF3C-gamma) General transcription factor 3C polypeptide 4 (EC 2.3.1 .48) (TF3C-delta) (Transcription Q9U N8 GTF3C4 factor MIC 90 kDa subunit) (TFIIIC 90 kDa 822 FALSE FALSE FALSE FALSE FALSE FALSE subunit) (TFIIIC90) (Transcription factor IC subunit delta) General transcription factor (GTFII-I) (TFII- I) (Bruton tyrosine kinase-associated protein 135) (BAP-135) (BTK-associated protein 135) P78347 GTF2I 398 TRUE TRUE TRUE TRUE TRUE FALSE (SRF-Phox1 -interacting protein) (SPIN) (Williams-Beuren syndrome chromosomal region 6 protein) General vesicular transport factor p 1 5 (Protein US01 homolog) (Transcytosis- 060763 US01 962 FALSE FALSE FALSE FALSE FALSE FALSE associated protein) (TAP) (Vesicle-docking protein) Glucose-6-phosphate 1-dehydrogenase P 1 1413 G6PD 515 TRUE FALSE FALSE FALSE FALSE FALSE (G6PD) (EC 1. 1 . 1 .49) Glucose-6-phosphate isomerase (GPI) (EC 5.3.1 .9) (Autocrine motility factor) (AMF) P06744 GP (Neuroleukin) (NLK) (Phosphoglucose 558 FALSE FALSE FALSE TRUE TRUE TRUE isomerase) (PGI) (Phosphohexose isomerase (PHI) (Sperm antigen 36) (SA-36) Giucosidase 2 subunit beta (80K-H protein) (Glucosidase subunit beta) (Protein kinase P14314 PRKCSH 528 FALSE FALSE FALSE FALSE FALSE FALSE C substrate 60.1 kDa protein heavy chain) (PKCSH) Glutamate dehydrogenase 1, mitochondrial P00367 GLUD1 558 FALSE FALSE FALSE TRUE TRUE TRUE (GDH 1) (EC 1.4.1 .3) Giutarnate-cysteine !igase regulatory subunit (GCS light chain) (Gamma-ECS regulatory P48507 GC subunit) (Gamma-g!utamylcysteine synthetase 274 TRUE TRUE TRUE FALSE FALSE TRUE regulatory subunit) (Giutarnate-cysteine ligase modifier subunit) G u a at -rich W D repeat-containing protein Q9BQ67 GRWD1 446 TRUE TRUE FALSE FALSE FALSE FALSE 1 Glutamine-~fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1 .16) (D-fructose-6-phosphate Q06210 GFPT1 amidotransferase 1) (Glutamine:fructose-6- 699 FALSE FALSE FALSE FALSE FALSE FALSE phosphate amidotransferase 1) (GFAT 1) (GFAT1) (Hexosephosphate aminotransferase 1) Glutamine-tRNA ligase (EC 6 .1.1.18) P47897 QARS 775 FALSE FALSE FALSE FALSE FALSE FALSE (Glutaminyl-tRNA synthetase) (GlnRS) Glutaredoxin-3 (PKC-interacting cousin of thioredoxin) (PICOT) (PKC-theta-interacting 076003 GLRX3 335 TRUE FALSE FALSE TRUE FALSE FALSE protein) (PKCq-interacting protein) (Thioredoxin-like protein 2) Glutathione reductase, mitochondrial (GR) P00390 GSR 522 FALSE FALSE FALSE FALSE. FALSE (GRase) (EC 1.8.1 .7) Glutathione S~transferase kappa 1 (EC 2.5.1 .18) (GST 13-13) (GST class-kappa) Q9Y2Q3 GSTK1 226 FALSE FALSE FALSE TRUE TRUE TRUE (GSTK1-1) (hGSTKI) (Glutathione S- transferase subunit 13)

Glutathione S-transferase omega-1 (GSTO-1) (EC 2.5.1 .18) (Glutathione S-transferase omega 1-1) (GSTO 1-1) (Giutathione- P78417 GSTQ1 dependent dehydroascorbate reductase) (EC 241 FALSE FALSE FALSE FALSE FALSE FALSE 1.8.5.1) (Monomethylarsonic acid reductase) ( A(V) reductase) (EC 1.20.4.2) (S- (Phenacyl)glutathione reductase) (SPG-R) Glutathione S-transferase P (EC 2.5.1 .18) P0921 1 GSTP1 210 FALSE FALSE FALSE FALSE FALSE FALSE (GST class-pi) (GSTP1-1) Glyceraldehyde-3-phosphate dehydrogenase P04406 GAPDH (GAPDH) (EC 1.2.1 .12) (Peptidyl-cysteine S- 335 FALSE FALSE FALSE FALSE FALSE FALSE nitrosylase GAPDH) (EC 2.6.99.-)

Glycine-tRNA ligase (EC 3.6.1.17) (EC 6.1 . 1 .14) (Diadenosine tetraphosphate P41250 GARS 739 FALSE FALSE FALSE FALSE FALSE FALSE synthetase) (AP-4-A synthetase) (Glycyl-tRNA synthetase) (GiyRS)

Glycogen debranching enzyme (Glycogen debrancher) [Includes: 4-alpha- glucanotransferase (EC 2.4.1 .25) (Oligo-1 ,4- P35573 AGL 1532 FALSE FALSE FALSE FALSE TRUE FALSE 1,4-glucantransferase); Amylo-alpha-1 ,6- glucosidase (Amy!o~1 ,6-g!ucosidase) (EC 3.2.1 .33) (Dextrin 6-aipha~D~glucosidase)]

Glycogen phosphorylase, brain form (EC P 1 1216 PYGB 843 FALSE FALSE FALSE FALSE FALSE FALSE 2.4.1 .1) Glycogen synthase kinase-3 alpha (GSK-3 P49840 GSK3A alpha) (EC 2.7.1 1.26) (Serine/threonine- 483 FALSE FALSE FALSE FALSE FALSE FALSE protein kinase GSK3A) (EC 2.7.1 1.1) Glycogen synthase kinase-3 beta (GSK-3 P49841 GSK3B beta) (EC 2.7.1 1.26) (Serine/threonine-protein 420 FALSE TRUE FALSE FALSE FALSE FALSE kinase GSK3B) (EC 2.7.1 1.1) Giycyipeptide N-tetradecanoyltransferase 1 (EC 2.3.1 .97) (Myristoyl-CoA:protein N- P30419 N T 1 myristoyltransferase 1) (N T 1) (Type N- 496 FALSE FALSE FALSE TRUE TRUE TRUE myristoyltransferase) (Peptide N- myristoyltransferase 1) Q9HC38 GLOD4 Glyoxalase domain-containing protein 4 313 FALSE FALSE FALSE FALSE FALSE FALSE Glyoxyiate reductase/hydroxypyruvate Q9UBQ7 GRHPR 328 FALSE FALSE FALSE FALSE FALSE FALSE reductase (EC 1.1.1 .79) (EC 1. 1 . 1 .81) G P synthase [glutamine-hydrolyzing] (EC P49915 G PS 6.3.5.2) (GMP synthetase) (Glutamine 693 TRUE TRUE TRUE FALSE FALSE FALSE amidotransferase) P0CG08 GPR89B Golgi H regulator B (Protein GPR 455 FALSE FALSE FALSE FALSE FALSE FALSE Golgi phosphoprotein 3 (Coat protein GPP34) Q9H4A6 GOLPH3 FALSE FALSE FALSE FALSE FALSE FALSE (Mitochondrial DNA absence factor) (MIDAS)

Golgi resident protein GCP80 (Acyl-CoA- binding domain-containing protein 3) (Golgi complex-associated protein 1) (GOCAP1) (Golgi phosphoprotein 1) (GOLPH1) (PBR- 39H3P7 ACBD3 528 FALSE FALSE FALSE FALSE FALSE FALSE and PKA-associated protein 7) (Peripheral benzodiazepine receptor-associated protein PAP7) [Cleaved into: Golgi resident protein GCP60, -ter inai y processed]

Golgi to ER traffic protein 4 homoiog (Conserved edge-expressed protein) Q7L5D6 GET4 327 TRUE FALSE FALSE FALSE FALSE FALSE (Transmembrane domain recognition complex 35 kDa subunit) (TRC35) Goigin subfamily A member 2 (130 kDa cis- QQ8379 GOLGA2 Golgi matrix protein) (GM130) (GM13Q 1002 TRUE TRUE FALSE TRUE TRUE FALSE autoantigen) (Golgin~95) GP transamidase component P!G-S Q96S52 PIGS (Phosphatidyiinositoi-glycan biosynthesis class 555 FALSE FALSE FALSE FALSE FALSE FALSE S protein) Growth factor receptor-bound protein 2 P62993 GRB2 (Adapter protein GRB2) (Protein Ash) 217 FALSE FALSE FALSE FALSE FALSE FALSE (SH2/SH3 adapter GRB2) GrpE protein homoiog 1, mitochondrial Q9HAV7 GRPEL1 217 FALSE FALSE FALSE TRUE TRUE TRUE (HMGE) (Mt-GrpE#1) GTP-binding nuclear protein Ran (Androgen receptor-associated protein 24) (GTPase Ran) P62826 RAN 216 FALSE FALSE FALSE FALSE FALSE FALSE (Ras-like protein TC4) (Ras-reiated nuclear protein) GTP-binding protein 1 (G-protein 1) (GP-1) OQ0178 GTPBP1 669 FALSE FALSE FALSE FALSE TRUE FALSE (GP1) GTP-binding protein Rheb (Ras homoiog Q15382 RHEB 184 FALSE FALSE FALSE FALSE FALSE FALSE enriched in brain) GTP-binding protein SAR1a (COP - Q9NR31 SAR1A 198 FALSE FALSE FALSE FALSE FALSE FALSE associated small GTPase) GTP-binding protein SAR1b (GTP-bindi Q9Y6B6 SAR1 B 198 TRUE FALSE FALSE FALSE FALSE FALSE protein B) (GTBPB)

P01 111 NRAS GTPase NRas (Transforming protein N-Ras) 189 TRUE FALSE FALSE FALSE FALSE FALSE GTPase-activating protein and VPS9 domain- Q14C86 GAPVD1 containing protein 1 (GAPex-5) (Rab5~ TRUE TRUE TRUE FALSE FALSE FALSE activating protein 6) Guanine nucleotide-binding protein G(i) GNAI2 subunit a pha 2 (Adenylate cyclase-inhibiting 355 FALSE FALSE FALSE FALSE FALSE FALSE G alpha protein) Guanine nucleotide-binding protein P62873 GNB1 G(i)/G(S)/G(T) subunit beta-1 (Transducin 340 FALSE FALSE FALSE FALSE FALSE FALSE beta chain 1) Guanine nucleotide-binding protein P62879 GNB2 G(i)/G(S)/G(T) subunit beta-2 (G protein 340 TRUE TRUE FALSE TRUE TRUE TRUE subunit beta-2) (Transducin beta chain 2) Guanine nucleotide-binding protein G(k) P08754 GNAI3 354 FALSE TRUE FALSE FALSE TRUE TRUE subunit alpha (G(i) alpha-3) Guanine nucleotide-binding protein G(q) P50148 GNAQ subunit alpha (Guanine nucleotide-binding 359 FALSE FALSE FALSE FALSE FALSE FALSE protein alpha-q) Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas (Adenylate Q5JWF2 G AS 1037 FALSE FALSE FALSE FALSE TRUE TRUE cyclase-stimulating G alpha protein) (Extra large alphas protein) (XLalphas) Guanine nucleotide-binding protein-like 1 P36915 GNL1 607 FALSE FALSE FALSE FALSE FALSE FALSE (GTP-binding protein HSR1) Guanine nucleotide-binding protein-like 3 (E2- induced gene 3 protein) (Novel nucleolar Q9BVP2 GNL3 549 FALSE FALSE FALSE TRUE TRUE FALSE protein 47) (NNP47) (Nucleolar GTP-binding protein 3) (Nucleostemin) H/ACA ribonucleoprotein complex subunit 1 G9NY12 GAR1 (Nucleolar protein family A member ) 217 FALSE FALSE FALSE FALSE FALSE FALSE (snoRNP protein GAR1) H/ACA ribonudeoprotein complex subunit 2 G9NX2^ NHP2 (Nucleolar protein family A member 2) 153 FALSE FALSE FALSE TRUE TRUE TRUE (snoRNP protein NHP2) H/ACA ribonudeoprotein complex subunii 4 (EC 5.4 99.-) (CBF5 homolog) (Dyskerin) 060832 DKC1 (Nopp140-associated protein of 57 kDa) 514 FALSE FALSE FALSE TRUE TRUE TRUE (Nucleolar protein NAP57) (Nucleolar protein family A member 4) (snoRNP protein DKC1) HAUS augmin-like complex subunit 1 (Coiled- Q96CS2 HAUS1 coil domain-containing protein 5) (Enhancer of 278 FALSE FALSE FALSE FALSE FALSE FALSE invasion-cluster) (HEI-C) Q9Y450 HBS1 L HBS1-iike protein (ERFS) 684 TRUE TRUE FALSE FALSE FALSE FALSE HEAT repeat-containing protein 1 (Protein BAP28) (U3 small nucleolar RNA-associated Q9H583 HEATR1 protein 0 homolog) [Cleaved into: HEAT 2144 FALSE FALSE TRUE TRUE TRUE FALSE repeat-containing protein , N-terminal!y processed] Heat shock 70 kDa protein 4 (HSP70-like Q0VDF9 HSPA14 509 FALSE TRUE FALSE TRUE TRUE TRUE protein 1) (Heat shock protein HSP80)

Heat shock 70 kDa protein 1B (Heat shock 70 P0D V9 HSPA1 B 641 FALSE FALSE FALSE FALSE FALSE FALSE kDa protein 2) (HSP70-2) (HSP70.2)

Heat shock 70 kDa protein 4 (HSP70RY) P34932 HSPA4 840 FALSE FALSE FALSE FALSE FALSE FALSE (Heat shock 70-related protein APG-2) Heat shock 70 kDa protein 4L (Heat shock 70- 095757 HSPA4L related protein APG-1) (Osmotic stress protein 839 FALSE FALSE FALSE FALSE FALSE FALSE 94) Heat shock cognate 7 1 kDa protein (Heat shock 70 kDa protein 8) (Lipopoiysaccharide- P 1 1142 HSPA8 646 FALSE FALSE FALSE FALSE FALSE FALSE associated protein 1) (LAP-1) (LPS-associated protein 1) Heat shock protein 105 kDa (Antigen NY-CO- Q92598 HSPH1 858 TRUE TRUE FALSE FALSE FALSE FALSE 25) (Heat shock 110 kDa protein) Heat shock proiein 75 kDa, mitochondria! (HSP 75) (TNFR-associated protein 1) (Tumor Q12931 TRAP1 704 FALSE FALSE FALSE FALSE FALSE FALSE necrosis factor type 1 receptor-associated protein) (TRAP-1) Heat shock protein beta-1 (HspB1) (28 kDa heat shock protein) (Estrogen-regulated 24 HSPB1 kDa protein) (Heat shock 27 kDa protein) 205 FALSE FALSE FALSE FALSE FALSE FALSE (HSP 27) (Stress-responsive protein 27) (SRP27) Heat shock protein HSP 90-alpha (Heat shock 86 kDa) (HSP 86) (HSP86) HSP90AA (Lipopoiysaccharide-associated protein 2) 732 FALSE FALSE FALSE FALSE FALSE FALSE 1 (LAP-2) (LPS-associated protein 2) (Renal carcinoma antigen NY-REN-38) HSP90AB Heat shock protein HSP 90-beta (HSP 90) P08238 724 FALSE FALSE! FALSE FALSE FALSE 1 (Heat shock 84 kDa) (HSP 84) (HSP84)

P30519 H OX2 Heme oxygenase 2 (HO-2) (EC 1.14.14.18 316 FALSE FALSE FALSE TRUE TRUE TRUE

Hemoglobin subunit alpha (Alpha-globin) P69905 HBA1 142 FALSE FALSEi FALSE! FALSE FALSE FALSE (Hemoglobin alpha chain) Hemoglobin subunit epsilon (Epsilon-globin) P02100 HBE1 147 FALSE FALSE A LSE FALSE FALSE FALSE (Hemoglobin epsilon chain)

Hemoglobin subunit gamma- 1 (Gamma-1- P69891 globin) (Hb F Agamma) (Hemoglobin gamma- 147 FALSE FALSE FALSE FALSE FALSE FALSE 1 chain) (Hemoglobin gamma-A chain)

Hemoglobin subunit zeta (HBAZ) (Hemoglobin HBZ 142 FALSE FALSE FALSE FALSE FALSE FALSE zeta chain) (Zeta-globin) Heparan sulfate 2-O-su!fotransferase 1 (2-0- Q7LGA3 HS2ST1 356 FALSE FALSE FALSE FALSE FALSE FALSE sulfotransferase) (20ST) (EC 2.8.2.-) Hepatoma-derived growth factor (HDGF) P51858 HDGF (High mobility group protein 1-like 2) (HMO 240 FALSE FALSE FALSE TRUE TRUE FALSE

' S L2) Hepatoma-derived growth factor-related Q7Z4V5 HDGFL2 protein 2 (HRP-2) (Hepatoma-derived growth 671 FALSE FALSE FALSE FALSE FALSE FALSE factor 2) (HDGF-2) ς u Heterochromatin protein -binding protein 3 553 TRUE TRUE TRUE TRUE TRUE TRUE b J H P o e in H P . B p74 Heterogeneous nuclear ribonucieoprotein A/B Q99729 ™ (hnRNP A/B) (APOBEC1 -binding protein 1) 332 FALSE FALSE FALSE FALSE FALSE FALSE (ABBP-1 ) HNRNPA Heterogeneous nuclear ribonucieoprotein A O Q 13 15 1 305 FALSE FALSE FALSE FALSE FALSE FALSE 0 (hnRNP AO)

Heterogeneous nuclear ribonucieoprotein A 1 (hnRNP A 1) (Helix-destabilizing protein) HNRNPA (Single-strand RNA-binding protein) (hnRNP P09651 372 FALSE FALSE FALSE FALSE FALSE FALSE 1 core protein A 1) [Cleaved into: Heterogeneous nuclear ribonucieoprotein A , N-terminaliy processed] HNRNPA Heterogeneous nuclear ribonucieoprotein A3 P51 991 378 FALSE FALSE FALSE FALSE FALSE FALSE 3 (hnRNP A3) Heterogeneous nuclear ribonucieoprotein D- HNRNPD like (hnRNP D-like) (hnRNP DL) (AU-rich 0 4979 F L3 Ε AL Ξ F L3 Ε F LS Ε FAL Ξ FAL3 EE L element RNA-binding factor) (JKT41 -binding protein) (Protein laAUFI ) Heterogeneous nuclear ribonucieoprotein D O HNRNPD (hnRNP DO) (AU-rich element RNA-binding 355 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) Heterogeneous nuclear ribonucieoprotein F (hnRNP F) (Nucieoiin-iike protein mcs94-1 ) P52597 HNRNPF 4 15 TRUE FALSE FALSE FALSE FALSE FALSE [Cleaved into: Heterogeneous nuclear ribonucieoprotein F, N-terminally processed] Heterogeneous nuclear ribonucieoprotein H HNRNPH (hnRNP H) [Cleaved into: Heterogeneous P3 943 9 FALSE FALSE FALSE FALSE FALSE FALSE 1 nuclear ribonucieoprotein H, N-terminaily processed] Heterogeneous nuclear ribonudeoprotein H2 (hnRNP H2) (FTP-3) (Heterogeneous nuclear HNRNPH ribonudeoprotein H') (hnRNP H') [Cleaved 449 FALSE FALSE FALSE FALSE FALSE FALSE into: Heterogeneous nuclear ribonudeoprotein H2, N-terminally processed]

Heterogeneous nuclear ribonudeoprotein H3 HNRNPH P31942 (hnRNP H3) (Heterogeneous nuclear 346 FALSE FALSE FALSE FALSE FALSE FALSE ribonudeoprotein 2H9) (hnRNP 2H9) Heterogeneous nuclear ribonudeoprotein K P61978 HNRNPK (hnRNP K) (Transformation up-regulated 463 FALSE FALSE FALSE FALSE FALSE FALSE nuclear protein) (TUNP) Heterogeneous nuclear ribonudeoprotein L P14866 HNRNPL 589 FALSE FALSE FALSE FALSE FALSE FALSE (hnRNP L)

. J . Heterogeneous nuclear ribonudeoprotein L- Q8WVV9 i - like (hnRNPLL) (Stromal RNA-regulating 542 FALSE FALSE FALSE FALSE FALSE FALSE factor) Heterogeneous nuclear ribonudeoprotein P52272 HNRNPH 730 FALSE FALSE FALSE FALSE FALSE FALSE (hnRNP M) Heterogeneous nuclear ribonudeoprotein Q (hnRNP Q) (Glycine- and fyrosine-rich RNA- 060506 SYNCRIP binding protein) (GRY-RBP) (NS1 -associated 623 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) (Synaptotagmin-binding, cytoplasmic RNA-interacting protein)

Heterogeneous nudear ribonudeoprotein R 633 FALSE FALSE FALSE FALSE FALSE FALSE (hnRNP R) Heterogeneous nuclear ribonudeoprotein U Q00839 HNRNPU (hnRNP U) (Scaffold attachment factor A) 825 FALSE FALSE FALSE FALSE FALSE FALSE (SAF-A) (p120) (pp120) Heterogeneous nudear ribonudeoprotein U- Q9BUJ2 HNRNPU like protein 1 (Adenovirus early region B- 356 FALSE FALSE FALSE FALSE FALSE FALSE L associated protein 5) (E B-55 kDa-associated protein 5) (E1 B-AP5) Heterogeneous nuclear ribonudeoprotein U- !ike protein 2 (Scaffold-attachment factor A2) 747 FALSE FALSE FALSE FALSE FALSE FALSE (SAF-A2) HNRNPA Heterogeneous nuclear nbonudeoproteins P22626 353 FALSE FALSE FALSE FALSE FALSE FALSE 2B1 A2/B1 (hnRNP A2/B1) Heterogeneous nuclear nbonudeoproteins P07910 HNRNPC 306 FALSE FALSE FALSE FALSE FALSE FALSE C1/C2 (hnRNP C1/C2) Hexokinase-1 (EC 2.7 1.1) (Brain form P19367 HK1 917 FALSE FALSE FALSE FALSE TRUE TRUE hexokinase) (Hexokinase type ) (HK ) High mobility group nucleosome-binding domain-containing protein 4 (Non-histone 000479 H GN4 90 FALSE FALSE FALSE FALSE FALSE FALSE chromosomal protein HMG-17-like 3) (Non histone chromosomal protein) High mobility group protein B 1 (High mobility P09429 HMGB1 215 FALSE FALSE FALSE FALSE FALSE FALSE group protein 1) (HMG-1) High mobility group protein B2 (High mobility P26583 H GB2 2 9 FALSE FALSE FALSE FALSE FALSE FALSE group protein 2) (HMG-2) High mobility group protein HMG-I/HMG-Y (HMG-I(Y)) (High mobility group AT-hook P17096 H GA 1 1 7 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) (High mobility group protein A1) (High mobility group protein R) Hippocaicin-like protein 1 (Calcium-binding P37235 HPCAL1 protein BDR-1) (HLP2) (Visinin-like protein 3) 193 FALSE FALSE FALSE FALSE FALSE FALSE (VILIP-3) Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) (Adenosine S'-monophosphoramidase) P49773 H T 1 126 FALSE FALSE FALSE FALSE FALSE FALSE (Protein kinase C inhibitor 1) (Protein kinase C- interacting protein 1) (PKC!-1)

Histidine-tRNA ligase, cytoplasmic (EC P12081 HARS 509 FALSE FALSE FALSE FALSE FALSE FALSE 6.1 . 1 .21) (Histidyl-tRNA synthetase) (HisRS) Histone acetyltransferase KAT7 (EC 2 3.1.48) (Histone acetyltransferase binding to ORC1) 095251 KAT7 (Lysine acetyltransferase 7) (MOZ, 6 11 FALSE FALSE FALSE FALSE FALSE FALSE YBF2/SAS3, SAS2 and TIP60 protein 2) (MYST-2) Histone acetyltransferase type B catalytic 014929 HAT1 subunif (EC 2.3.1.48) (Histone 419 FALSE FALSE FALSE FALSE FALSE FALSE acetyltransferase 1)

Q 13547 HDAC1 Histone deacetyiase 1 (HD1) (EC 3.5.1 .98) 482 FALSE TRUE TRUE TRUE TRUE TRUE

Q92769 HDAC2 Histone deacetyiase 2 (HD2) (EC 3.5.1 .98) 488 TRUE TRUE FALSE TRUE FALSE TRUE

Histone deacetyiase complex subunit SAP1i (18 Da Sin3-associated polypeptide) OQ0422 SAP 18 153 FALSE FALSE FALSE FALSE FA LS FALSE (2HOR0202) (Cell growth-inhibiting gene 38 protein) (Sin3-associated polypeptide p18)

H1ST1 H 1 Hisione H 1.2 (Histone H1c) (Histone H1d) P16403 213 F S ! F L FA L E F L FALSE FALSE C (Histone H1s-1) H1ST1 H 1 P16402 Histone H 1.3 (Histone H1c) (Histone H1s-2) 221 FA L ! FALSE FALSE F LSE FALSE FALSE D H1ST1 H 1 Hisione H 1.5 (Histone H1a) (Histone H1b) P16401 226 L FALSE FA L E FA L FALSE FALSE B (Histone H1s-3) H 1FX Histone H1x 213 FALSE FALSE FALSE FALSE FALSE FALSE HIST1 H2 Histone H2A type 1-B/E (Histone H2A.2) P04908 130 FALSE FALSE FALSE FA L E FALSE FALSE A B (Histone H2A/a) (Histone H2A/m) HIST2H2 Histone H2A type 2-A (Histone H2A.2) Q6FM3 130 FALSE FALSE FALSE FA L E FALSE FALSE AA3 (Histone Η2Α Ό) HIST2H2 Q8IUE6 Histone H2A type 2-B 130 FALSE FALSE FALSE FA L E FALSE FALSE A B P0C0S5 H2AFZ Histone H2A.Z (H2A/z) 128 FALSE FALSE FALSE FALSE FALSE FALSE P16104 H2AFX Histone H2AX (H2a/x) (Histone H2A.X) 143 FALSE FALSE FALSE FALSE FALSE FALSE HIST1 H2 Histone H2B type 1-K (H2B K) (HIRA- 060814 126 FALSE FALSE FALSE FALSE FALSE FALSE interacting protein 1) Histone H3.1 (Histone H3/a) (Histone H3/b) H ST H3 (Histone H3/c) (Histone H3/d) (Histone H3/f) P68431 136 FALSE FALSE FALSE FALSE FALSE FALSE A (Histone H3/h) (Histone H3/i) (Histone H3/j) (Histone H3/k) (Histone H3/I)

HIST2H3 Q7 DI3 Histone H3.2 (Histone H3/m) (Histone Η3/Ό) 136 FALSE FALSE FALSE FALSE FALSE FALSE A ; P84243 H3F3A Histone H3.3 136 FALSE FALSE FALSE FALSE FALSE FALSE HIST1H4 P62805 Histone H4 103 FALSE FALSE FALSE FALSE FALSE FALSE A Histone-arginine methyitransferase CA R 1 (EC 2.1 . 1 .319) (Coactivator-associated Q86X55 CAR 1 6 8 FALSE FALSE FALSE TRUE FALSE TRUE arginine methyitransferase 1) (Protein arginine N-methyltransferase 4) Histone-binding protein RBBP4 (Chromatin assembly factor 1 subunit C) (CAF-1 subunit C) (Chromatin assembly factor p48 subunit) (CAF-I 48 kDa subunit) (CAF-I p48) Q09028 RBBP4 425 FALSE FALSE FALSE TRUE TRUE TRUE (Nucleosome-remodeiing factor subunit RBAP48) (Retinoblastoma-binding protein 4) (RBBP-4) (Retinoblastoma-binding protein p48) Histone-binding protein RBBP7 (Histone acetyitransferase type B subunit 2) (Nucleosome-remodeiing factor subunit Q16576 RBBP7 425 FALSE FALSE FALSE TRUE TRUE TRUE RBAP46) (Retinoblastoma-binding protein 7) (RBBP-7) (Retinoblastoma-binding protein

043719 HTATSF1 HIV Tat-specific factor 1 (Tat-SF1) 755 FALSE FALSE FALSE FALSE FALSE FALSE Host cell factor 1 (HCF) (HCF-1) (C1 factor) (CFF) (VCAF) (VP18 accessory proiein) [Cleaved into: HCF N-terminal chain 1; HCF N- terminal chain 2 ; HCF N-terminal chain 3 ; HCF P51610 HCFC1 N-terminal chain 4 ; HCF N-terminal chain 5 ; 2035 FALSE FALSE FALSE FALSE FALSE FALSE HCF N-ferminal chain 6 ; HCF C-terminai chain 1; HCF C-terminal chain 2 ; HCF C-terminal chain 3 ; HCF C-terminal chain 4 ; HCF C- terminal chain 5 ; HCF C-terminal chain 6]

Hsc70-interacting proiein (Hip) (Aging- associated protein 2) (Progesterone receptor- Q associated p48 protein) (Protein FAM10A1) P505Q2 369 FALSE FALSE FALSE FALSE FALSE FALSE (Putative tumor suppressor ST13) (Renal carcinoma antigen NY-REN-33) (Suppression of tumorigenicity 13 protein)

Hsp70-binding protein 1 (HspBPI) (Heat shock protein-binding protein 1) (Hsp70- Q9NZL4 HSPBP1 binding protein 2) (HspBP2) (Hsp7Q- 362 TRUE FALSE FALSE FALSE FALSE FALSE inferacting protein 1) (Hsp70-interacting protein 2)

Hsp9Q co-chaperone Cdc37 (Hsp9Q chaperone protein kinase-targeting subunit) Q16543 CDC37 378 FALSE FALSE FALSE FALSE FALSE FALSE (p50Cdc37) [Cleaved into: Hsp90 co- chaperone Cdc37, N-terminally processed]

Hydroxyacyi-coenzyme A dehydrogenase, mitochondrial (HCDH) (EC 1. 1 1 .35) (Medium Q16836 HADH and short-chain L-3-hydroxyacyl-coenzyme A 314 FALSE FALSE FALSE TRUE FALSE TRUE dehydrogenase) (Short-chain 3-hydroxyacyi- CoA dehydrogenase) Hydroxymethylglutaryl-CoA synthase, cytoplasmic (HMG-CoA synthase) (EC QQ1581 H GCS1 520 FALSE FALSE FALSE FALSE FALSE FALSE 2.3.3.10) (3-hydroxy-3-methyiglutaryl coenzyme A synthase) Hypoxanthine-guanine P00492 HPRT1 phosphoribosyltransferase (HGPRT) 218 TRUE FALSE FALSE FALSE FALSE FALSE (HGPRTase) (EC 2.4.2 8) Hypoxia up-regulated protein 1 (150 kDa Q9Y4L1 HYOU1 oxygen-regulated protein) (ORP-150) (170 999 FALSE FALSE FALSE FALSE TRUE FALSE kDa glucose-regulated protein) (GRP-170) Immediate early response 3-interacting protein Q9Y5U9 IER3IP1 82 FALSE FALSE FALSE FALSE FALSE FALSE 1 !mportin subunit a pha- (Karyopherin subunit P52292 KPNA2 529 FALSE FALSE FALSE FALSE FALSE FALSE alpha-2) (RAG cohort protein 1) (SRP1 -alpha) Importin subunit alpha-3 (Importin alpha Q1) 000629 KPNA4 521 TRUE TRUE TRUE TRUE FALSE TRUE (Qip1) (Karyopherin subunit alpha-4) Importin subunit alpha-5 (Karyopherin subunit alpha-1) (Nucleoprotein interactor 1) (NPI-1) P52294 KPNA1 (RAG cohort protein 2) (SRP1-beta) [Cleaved 538 FALSE TRUE FALSE FALSE FALSE FALSE into: Importin subunit alpha-5, N-terminally processed] Importin subunit aipha-7 (Karyopherin subunit 060684 KPNA6 536 TRUE TRUE TRUE FALSE TRUE FALSE alpha-6) Importin subunit beta-1 (lmportin~90) (Karyopherin subunit beta-1) (Nuclear factor Q14974 KPNB1 876 FALSE FALSE FALSE FALSE FALSE FALSE p97) (Pore targeting complex 97 kDa subunit) (PTAC97) lmportin-4 (Imp4) (lmportin-4b) (Imp4b) (Ran- Q8TEX9 Ρ0 4 1081 FALSE TRUE FALSE TRUE TRUE TRUE binding protein 4) (RanBP4) lmportin-5 ( pS) (Importin subunit beta-3) 000410 IPOS (Karyopherin beta-3) (Ran-binding protein 5) 1097 FALSE TRUE FALSE TRUE TRUE FALSE (RanBPS) lmportin-7 (Imp7) (Ran-binding protein 7) 095373 1P07 1038 FALSE FALSE FALSE FALSE FALSE TRUE (RanBP7) lmportin-8 (ImpS) (Ran-binding protein 8) 015397 IPOS 1037 FALSE FALSE FALSE FALSE FALSE FALSE (RanBPS) lmportin-9 (Imp9) (Ran-binding protein 9) Q96P70 1P09 FALSE FALSE FALSE FALSE FALSE FALSE (RanBP9) Inner nuclear membrane protein an1 (LE Q9Y2U8 LE D3 9 11 FALSE FALSE TRUE FALSE FALSE FALSE domain-containing protein 3) Inorganic pyrophosphatase (EC 3.6 1.1) Q15181 PPA1 289 FALSE FALSE FALSE FALSE FALSE FALSE (Pyrophosphate phospho-hydrolase) (PPase)

Inosine-S'-monophospbate dehydrogenase 2 P12268 IMPDH2 (IMP dehydrogenase 2) (i PD 2) (IMPDH 2) 514 FALSE FALSE FALSE FALSE FALSE FALSE (EC 1. 1 . 1 .205) (IMPDH-II) Insulin-degrading enzyme (EC 3.4.24.56) P14735 IDE (Abeta-degrading protease) (insulin protease) 1019 FALSE FALSE FALSE FALSE FALSE FALSE ( su inase) (insulysin) Insulin-like g h factor 2 mRNA-binding protein 1 (IGF2 mRNA-binding protein 1) (I P- 1) (IMP1) (Coding region determinant-binding Q9NZI8 IGF2BP1 577 FALSE FALSE FALSE FALSE FALSE FALSE protein) (CRD-BP) (IGF-ii mRNA-binding protein 1) (VICKZ family member 1) (Zipcode- binding protein 1) (ZBP-1) Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2 mRNA-binding protein 3) (I P- 000425 IGF2BP3 3) (IGF-II mRNA-binding protein 3) (KH 579 FALSE FALSE FALSE FALSE FALSE FALSE domain-containing protein overexpressed in cancer) (hKOC) (VICKZ family member 3) Q9NVH2 INTS7 Integrator complex subunit 7 (Int7) 962 FALSE FALSE TRUE FALSE FALSE FALSE Integrator complex subunit 8 (Int8) (Protein Q75QN2 INTS8 995 FALSE FALSE FALSE FALSE FALSE FALSE kaonashi-1) Integrin-linked kinase-associated Q9H0C8 ILKAP serine/threonine phosphatase 2C (ILKAP) (EC 392 FALSE FALSE FALSE FALSE FALSE TRUE 3.1 .3.16) Interferon-inducible doubie-stranded RNA- dependent protein kinase activator A (PKR- associated protein X) (PKR~associating 075569 PRKRA protein X) (Protein activator of the interferon- 313 FALSE FALSE FALSE FALSE TRUE FALSE induced protein kinase) (Protein kinase, interferon-inducible double-stranded RNA- dependent activator)

Interleukin enhancer-binding factor 2 (Nuclear Q 12905 LF2 390 FALSE FALSE FALSE FALSE FALSE FALSE factor of activated T-ce s 45 kDa)

Interleukin enhancer-binding factor 3 (Double- stranded RNA-binding protein 76) (DRBP76) (M-phase phosphoprotein 4) (MPP4) (Nuclear Q12906 LF3 factor associated with dsRNA) (NFAR) 894 FALSE FALSE FALSE FALSE FALSE FALSE (Nuclear factor of activated T-cells 90 kDa) (NF-AT-90) (Translafional control protein 80) (TCP80) ntraflagellar transport protein 25 homolog Q9Y547 HSPB1 1 (Heat shock protein beta-1 1) (Hspbl 1) 144 FALSE FALSE FALSE FALSE FALSE FALSE (Placental protein 25) (PP25) Intron-binding protein aquarius (intron-binding 060306 AQR 1485 FALSE FALSE FALSE TRUE TRUE TRUE protein of 160 kDa) (IBP160)

Q96CN7 1SOC1 Isochorismatase domain-containing protein 1 298 FALSE FALSE FALSE FALSE FALSE FALSE

Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1 1.1.41) (Isocitric P50213 H3A 366 TRUE TRUE FALSE FALSE TRUE TRUE dehydrogenase subunit alpha) (NAD(+)- specific CDH subunit alpha) Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial (EC 1.1.1 .41) (Isocitric 043837 1DH3B 385 FALSE FALSE FALSE TRUE FALSE TRUE dehydrogenase subunit beta) (NAD(-s-)-specific CDH subunit beta) Isocitrate dehydrogenase [NADP] cytoplasmic (IDH) (EC 1. 1 1.42) (Cytosoiic NADP-isocitrate 075874 IDH1 414 FALSE FALSE FALSE TRUE FALSE FALSE dehydrogenase) ( IDP) (NADP(+)-specific !CDH) (Oxaiosuccinate decarboxylase)

Isocitrate dehydrogenase [NADP], mitochondrial (IDH) (EC 1.1 . 1 .42) (ICD-M) P48735 DH2 452 FALSE FALSE FALSE FALSE FALSE FALSE ( IDP) (NADP(-H)-specific ICDH) (Oxaiosuccinate decarboxylase) Isoleucine-tRNA ligase, cytoplasmic (EC P41252 IARS 6.1 . 1 .5) (Iso!eucyi-tRNA synthetase) (IRS) 1262 FALSE FALSE FALSE FALSE FALSE FALSE ( i RS)

Isoleucine-tRNA ligase, mitochondrial (EC Q9NSE4 IARS2 1012 TRUE FALSE FALSE FALSE. FALSE 6.1 . 1 .5) (Isoieucyi-tRNA synthetase) (HeRS)

Isopentenyl-diphosphate Deita-isomerase 1 Q13907 IDI1 (EC 5.3.3.2) (Isopentenyi pyrophosphate 227 FALSE FALSE FALSE TRUE TRUE TRUE isomerase 1) ( PP isomerase 1) (!PP! ) Junction piakogiobin (Catenin gamma) P14923 JUP 745 FALSE F L FALSEE FALSE. FALSEi FALSE (Desmoplakin III) (Desmoplakin-3) Keratin, type cytoskeietai 14 (Cytokeratin-14) P02533 KRT14 472 FALSE FALSE FALSE FALSE FALSE FALSE (CK-14) (Keratin-14) (K14) Keratin, type cytoskeietai 1b (Cytokeratin- Q7Z794 KRT77 1B) (CK-1 B) (Keratin-77) (K77) (Type- 578 FALSE FALSE FALSE FALSE FALSE FALSE keratin Kb39) KH domain-containing, RNA-binding, signal transduction-associated protein 1 (GAP- KHDRBi associated tyrosine phosphoprotein p62) (Src- QQ7666 443 FALSE FALSE FALSE TRUE FALSE FALSE 1 associated in mitosis 68 kDa protein) (Sam68) (p21 Ras GTPase-activating protein- associated p62) (p68) Q96EK5 KIF1BP KIF1-binding protein 621 FALSE FALSE FALSE TRUE FALSE TRUE Q86UP2 KTN1 Kinectin (CG-1 antigen) (Kinesin receptor) 1357 TRUE FALSE FALSE TRUE FALSE FALSE KLC1 Kinesin light chain 1 (KLC 1) 573 FALSE FALSE FALSE FALSE FALSE FALSE Kinesin~1 heavy chain (Conventional kinesin P33176 KIF5B heavy chain) (Ubiquitous kinesin heavy chain) 963 FALSE FALSE FALSE FALSE FALSE FALSE (UKHC) Kinesin-like protein K IF 1 1 (Kinesin-like protein 1) (Kinesin-like spindle protein HKSP) (Kinesin- P52732 K IF 1 1 related motor protein Eg5) (Thyroid receptor- 1056 TRUE FALSE FALSE FALSE TRUE FALSE interacting protein 5) (TR-interacting protein 5) (TR!P-5)

Kinesin-like protein KIF22 (Kinesin-like DNA- Q 14807 K1F22 665 FALSE FALSE TRUE FALSE FALSE TRUE binding protein) (Kinesin-like protein 4)

Kinesin-like protein K1F23 (Kinesin-like protein Q02241 KIF23 960 FALSE FALSE FALSE FALSE FALSE TRUE 5) (Mitotic kinesin-like protein 1)

000139 KIF2A Kinesin-like protein KIF2A (Kinesin-2) (hK2) 7 6 FALSE TRUE FALSE TRUE TRUE FALSE

Kinesin-like protein K1F2C (Kinesin-like protein Q99661 KIF2C 6) (Mitotic centromere-associated kinesin) 725 FALSE FALSE FALSE TRUE TRUE TRUE ( CA K) Kinesin-like protein K1FC1 (Kinesin-like protein Q9BW19 K1FC1 673 FALSE FALSE FALSE FALSE FALSE FALSE 2) (Kinesin-reiated protein HSET) Q8NBT2 SPC24 Kinetochore protein Spc24 (hSpc24) 197 FALSE FALSE FALSE FALSE FALSE FALSE

Krueppel-like factor 16 (Basic transcription element-binding protein 4) (BTE-binding Q9BXK1 KLF16 protein 4) (Novel Sp1-like zinc finger 252 FALSE FALSE FALSE FALSE FALSE FALSE transcription factor 2) (Transcription factor BTEB4) (Transcription factor NSLP2)

Kynurenine-oxoglutaraie transaminase 3 (EC 2.6.1 7) (Cysteine-S-conjugate beta-lyase 2) (EC 4.4.1 .13) (Kynurenine aminotransferase Q6YP21 KYAT3 3) (Kynurenine aminotransferase III) (KAT ) FALSE FALSE FALSE FALSE FALSE FALSE (Kynurenine-glyoxyiate transaminase) (EC 2.6. 1.63) (Kynurenine-oxogiutarate transaminase i) L-aminoadipate-serrsialdehyde dehydrogenase- phosphopanteiheinyl transferase (EC 2 7.8.~) AASDHP (4'-phosphopantetheinyl transferase) (Alpha- 309 TRUE TRUE TRUE TRUE TRUE FALSE PT aminoadipic semialdehyde dehydrogenase- phosphopanietheinyl transferase) (AASD- PPT) (LYS5 ortholog)

L-lactate dehydrogenase A chain (LDH-A) (EC 1. 1 . 1 .27) (Cell proliferation-inducing gene 19 P00338 LDHA 332 FALSE FALSE FALSE FALSE FALSE FALSE protein) (LDH muscle subunit) (LDH-M) (Renal carcinoma antigen NY-REN-59) L-lactate dehydrogenase B chain (LDH-B) (EC P07195 LDHB 1. 1 . 1 .27) (LDH heart subunit) (LDH-H) (Renal 334 FALSE FALSE FALSE FALSE FALSE FALSE carcinoma antigen NY-REN-46) L-xyiulose reductase (XR) (EC 1. 1 . 1 .10) (Carbonyl reductase ) (Dicarbonyl/L-xylulose reductase) (Kidney dicarbonyi reductase) Q7Z4W1 DCXR 244 FALSE FALSE FALSE FALSE FALSE FALSE (kiDCR) (Short chain dehydrogenase/reductase family 20C member 1) (Sperm surface protein P34H) La-related protein 1 (La ribonucieoprotein Q6PKG0 LARP1 1096 FALSE FALSE FALSE FALSE FALSE FALSE domain family member 1)

Lactoyiglutathione lyase (EC 4.4.1 .5) (Aldoketomutase) (Glyoxaiase i) (G x ) GL01 184 FALSE FALSE FALSE FALSE FALSE FALSE (Ketone-aldehyde mutase) (Methylglyoxalase) (S-D-lactoylglutathione methylglyoxai lyase)

Lamin-B receptor (Integral nuclear envelope Q14739 615 FALSE FALSE FALSE FALSE FALSE FALSE inner membrane protein) (LMN2R)

P20700 LMNB1 Lamin-B1 586 FALSE FALSE FALSE FALSE FALSE FALSE Q03252 LMNB2 Lamin-B2 620 TRUE FALSE TRUE TRUE TRUE FALSE Lamina-associated polypeptide 2 , isoform alpha (Thymopoietin isoform alpha) (TP alpha) P42166 T PO (Thymopoietin-related peptide isoform alpha) 694 FALSE FALSE FALSE FALSE FALSE FALSE (TPRP isoform alpha) [Cleaved into: Thymopoietin (TP) (Splenin); Thymopentin (TPS)] Lamina-associated polypeptide 2 , isoforms beta/gamma (Thymopoietin, isoforms beta/gamma) (TP beta/gamma) (Thymopoietin- P42167 TMPO related peptide isoforms beta/gamma) (TPRP 454 FALSE FALSE FALSE FALSE FALSE FALSE isoforms beta/gamma) [Cleaved into: Thymopoietin (TP) (Splenin); Thymopentin (TP5)] Lanosterol 14-alpha demethylase (LDM) (EC 1.14.13.70) (CYPLl) (Cytochrome P450 51A1) Q16850 CYP51A1 (Cytochrome P450-14DM) (Cytochrome 503 FALSE FALSE FALSE TRUE FALSE FALSE P45014DM) (Cytochrome P450LI) (Sterol 14- alpha demethylase) Lanosterol synthase (EC 5.4.99.7) (2,3- epoxysquaiene-lanosterol cyclase) P48449 LSS 732 FALSE TRUE FALSE TRUE TRUE TRUE (Oxidosqualene-lanosterol cyclase) (OSC) (hOSC) Large neutral amino acids transporter small subunit 1 (4F2 light chain) (4F2 LC) (4F2LC) (CD98 light chain) (Integral membrane protein Q01650 SLC7A5 507 FALSE FALSE FALSE FALSE FALSE FALSE E16) (L-type amino acid transporter 1) (hLAT1) (Solute carrier family 7 member 5) (y+ system cationic amino acid transporter) Large proline-rich protein BAG6 (BAG family molecular chaperone regulator 6) (BCL2- P46379 BAG6 associated athanogene 6) (BAG-6) (HLA-B- 1132 TRUE FALSE TRUE FALSE FALSE TRUE associated transcript 3) (Protein G3) (Protein Scythe) Late cornified envelope protein 2B (Late envelope protein 10) (Skin-specific protein 0 4633 LCE2B 110 FALSE FALSE FALSE FALSE FALSE FALSE Xp5) (Small proiine-rich-like epidermal differentiation complex protein 1B) Mitochondrial proton/calcium exchanger 095202 LET 1 protein (Leucine zipper-EF-hand-containing 739 TRUE TRUE TRUE FALSE FALSE FALSE transmembrane protein 1)

Leucine-tRNA ligase, cytoplasmic (EC Q9P2J5 LARS 1176 FALSE FALSE FALSE FALSE FALSE FALSE 6.1 . 1 .4) (Leucyl-tRNA synthetase) (LeuRS)

Leucine-rich PPR motif-containing protein, LRPPRC mitochondrial (130 kDa leucine-rich protein) 1394 TRUE TRUE FALSE TRUE TRUE TRUE (LRP 130) (GP130)

Leucine-rich repeat and W D repeat-containing protein 1 (Centromere protein 33) (CENP-33) Q9UFC0 LRWD1 647 FALSE FALSE FALSE FALSE FALSE FALSE (Origin recognition complex-associated protein) (ORC-associated protein) (ORCA) oo Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 583 FALSE FALSE FALSE FALSE FALSE FALSE Leucine-rich repeat-containing protein 59 Q96AG4 LRRC59 307 FALSE FALSE FALSE FALSE FALSE FALSE (Ribosome-binding protein p34) (p34) Q96PV6 LENG8 Leukocyte receptor duster member 8 779 FALSE FALSE FALSE FALSE FALSE FALSE LIM and SH3 domain protein 1 (LASP-1) Q 14847 LASP1 (Metastatic lymph node gene 50 protein) (MLN 261 FALSE FALSE FALSE FALSE FALSE FALSE 50)

Lipase maturation factor 2 (Transmembrane Q9BU23 L F2 707 FALSE FALSE FALSE FALSE FALSE FALSE protein 112B) (Transmembrane protein 153)

Lipid droplet-associated hydrolase (EC 3.1 . 1 .-) Q9H6V9 LDAH (Lipid droplet-associated serine hydrolase) 325 TRUE TRUE FALSE FALSE FALSE FALSE (hLDAH) Lipopolysaccharide-responsive and beige-like P50851 LRBA anchor protein (Beige-like protein) (CDC4-like 2863 FALSE FALSE! FALSE FALSE protein) Lon protease hornolog, mitochondrial (EC 3.4.21.-) (LONHs) (Lon protease-!ike protein) P36776 LONP1 959 FALSE FALSE FALSE TRUE TRUE TRUE (LONP) (Mitochondria! ATP-dependent protease Lon) (Serine protease 15) Long-chain-fatty-acid--CoA ligase 3 (EC 095573 ACSL3 6.2.1 .3) (Long-chain acyi-CoA synthetase 3) 720 FALSE FALSE FALSE FALSE FALSE FALSE (LACS 3) Long-cbain-fatty-acid-CoA iigase 4 (EC 060488 ACSL4 6.2.1 .3) (Long-chain acyi-CoA synthetase 4) 7 11 FALSE FALSE FALSE FALSE FALSE FALSE (LACS 4) Low molecular weight phosphotyrosine protein phosphatase (LMW-PTP) (LMW-PTPase) (EC P24666 ACP1 3.1 .3.48) (Adipocyte acid phosphatase) (Low 158 FALSE TRUE FALSE FALSE FALSE FALSE molecular weight cytosolic acid phosphatase) (EC 3.1 .3.2) (Red cell acid phosphatase 1) Luc7-like protein 3 (Cisplatin resistance- associated-overexpressed protein) (Luc7A) (Okadaic acid-inducible phosphoprotein OA48- 095232 LUC7L3 432 FALSE FALSE FALSE FALSE FALSE FALSE 18) (cA P regulatory element-associated protein 1) (CRE-associated protein 1) (CREAP- 1) Lupus La protein (La autoantigen) (La P05455 SSB ribonucleoprotein) (Sjoegren syndrome type B 408 TRUE FALSE FALSE FALSE FALSE FALSE antigen) (SS-B) Lympbokine-activated killer T-cell-originated protein kinase (EC 2.7 12.2) (Cancer/testis antigen 84) (CT84) (MAPKK-like protein Q96KB5 PBK 322 TRUE FALSE FALSE FALSE FALSE FALSE kinase) (Nori-3) (PDZ-binding kinase) (Spermatogenesis-related protein kinase) (SPK) (T-LAK cell-originated protein kinase)

Lysine-tRNA ligase (EC 6.1 . 1 .6) (Lysyl-tRNA Q15046 KARS 597 FALSE FALSE FALSE FALSE FALSE FALSE synthetase) (LysRS) Lysine-specific histone demeihylase 1A (EC 1 .- -) (BRAF35-HDAC complex protein 060341 KDM1A 852 TRUE TRUE TRUE TRUE TRUE TRUE BHC1 10) (Flavin-containing amine oxidase domain-containing protein 2)

Q5WVZ2 LYPLAL1 Lysophospholipase-like protein 1 (EC 3.1 .2. 237 FALSE FALSE FALSE FALSE FALSE FALSE

Lysophospholipid acyltransferase 7 (LPLAT 7) (EC 2.3.1 .-) (1-acylglycerophosphatidylinositol O-acyltransferase) (EC 2.3.1 .n4) (Bladder and breast carcinoma-overexpressed gene 1 protein) (Leukocyte receptor cluster member Q96N66 BOAT7 472 FALSE FALSE FALSE FALSE TRUE TRUE 4) (Lysophosphatidylinositoi acyltransferase) (LPIAT) (Lyso-PI acyltransferase) (Membrane- bound O-acyltransferase domain-containing protein 7) (O-acyltransferase domain- containing protein 7) (h-mboa-7) o9 Macrophage migration inhibitory factor (MIF) (EC 5.3.2.1) (Glycosyiation-inhibiting factor) P14174 (GIF) (L-dopachrome isomerase) (L- 115 FALSE FALSE FALSE FALSE FALSE FALSE dopachrome taufomerase) (EC 5.3.3.12) (Phenylpyruvate tautomerase) Magnesium transporter protein 1 (MagT1) Q9H0U3 MAGT1 335 FALSE TRUE FALSE TRUE TRUE FALSE (implantation-associated protein) (IAP) Malate dehydrogenase, cytoplasmic (EC I .1. 1 .37) (Cytosoiic malate dehydrogenase) P40925 MDH1 334 FALSE FALSE FALSE FALSE FALSE FALSE (Diiodophenylpyruvate reductase) (EC I .1.96) Malate dehydrogenase, mitochondrial (EC P40926 MDH2 338 FALSE FALSE FALSE FALSE FALSE FALSE 1. 1 . 1 .37) Q14165 MLEC Malectin FALSE FALSE FALSE FALSE FALSE FALSE Malignant T-ceil-amplified sequence 1 (MCT- Q9ULC4 CTS1 181 FALSE FALSE FALSE FALSE FALSE FALSE 1) (Multiple copies T-cell malignancies) Manganese-transporting ATPase 13A1 (EC Q9HD20 ATP13A1 1204 FALSE FALSE FALSE TRUE TRUE FALSE 3.6.3 -) Mannose-P-dolichol utilization defect 1 protein 075352 (Suppressor of Le 5 and Lec35 glycosylation 247 TRUE FALSE FALSE TRUE TRUE FALSE mutation homo!og) (SL15)

Mannosyl-oligosaccharide glucosidase (EC Q 13724 0 GS 837 FALSE FALSE FALSE FALSE FALSE TRUE 3.2.1 .106) (Processing A-glucosidase )

MARCKS-reiated protein (MARCKS-like MARCKS protein 1) (Macrophage myristoyiated alanine- P49006 195 FALSE FALSE! FALSE FALSE! FALSE L 1 rich C kinase substrate) (Mac-MARCKS) (MacMARCKS) Maspardin (Acid cluster protein 33) (Spastic paraplegia 2 1 autosomal recessive Mast Q9NZD8 SPG21 3 8 FALSE F LS E FALSE! FALSE FALSE FALSE syndrome protein) (Spastic paraplegia 2 1 protein) P43243 1ATR3 Matrin-3 847 FALSE FALSE FALSE FALSE FALSE FALSE

Mediator of DNA damage checkpoint protein 1 Q 14676 1DC1 2089 FALSE FALSE FALSE FALSE FALSE FALSE (Nuclear factor with BRCT domains 1)

Mediator of RNA polymerase transcription Q9Y3C7 subunit 3 1 (Mediator complex subunit 31) 131 FALSE FALSE FALSE FALSE FALSE FALSE (Mediator complex subunit SOH1) (hSOH1)

Medium-chain specific acyl-CoA P 1 1310 ACADIA dehydrogenase, mitochondrial (MCAD) (EC 421 FALSE FALSE FALSE FALSE FALSE FALSE 1.3.8.7)

Melanoma-associated antigen D2 ( 1 1B6) (Breast cancer-associated gene 1 protein) Q9UNF1 A G ED2 606 TRUE FALSE FALSE FALSE FALSE FALSE (BCG-1) (Hepatocellular carcinoma- associated protein JCL-1) (MAGE-D2 antigen)

Membrane magnesium transporter 1 (ER Q8N4V1 GT 1 membrane protein complex subunit 5) 131 FALSE FALSE FALSE TRUE FALSE TRUE (Transmembrane protein 32) Membrane-associated progesterone receptor OQ0264 PGR C1 195 TRUE TRUE FALSE TRUE TRUE TRUE component 1 (mPR) Membrane-associated progesterone receptor 015173 PGRMC2 component 2 (Progesterone membrane- 223 FALSE FALSE FALSE FALSE FALSE FALSE binding protein) (Steroid receptor protein DG6) Q13330 MTA1 Metastasis-associated protein MTA1 715 FALSE FALSE FALSE TRUE FALSE TRUE Metastasis-associated protein MTA2 (Metastasis-associated 1-iike 1) (MTA1-L1 094776 MTA2 668 FALSE FALSE FALSE FALSE FALSE FALSE protein) (p53 target protein in deacetyiase complex) Metaxin-1 (Mitochondria! outer membrane Q13505 MTX1 466 FALSE FALSE FALSE TRUE FALSE FALSE import complex protein 1) Metaxin-2 (Mitochondria! outer membrane 075431 MTX2 263 FALSE FALSE FALSE FALSE FALSE FALSE import complex protein 2) Methionine adenosy!transferase 2 subunit beta (Methionine adenosyltransferase ! beta) Q9NZL9 MAT2B 334 TRUE FALSE FALSE TRUE TRUE TRUE (MAT beta) (Putative dTDP-4-keto-6-deoxy- 9 D-glucose 4~reductase) Methionine aminopeptidase 1 (MAP 1) (MetAP P53582 IETAP1 386 FALSE FALSE FALSE TRUE FALSE FALSE ) (EC 3 4. .18) (Peptidase M 1) Methionine aminopeptidase 2 (MAP 2) (MetAP 2) (EC 3 4. .18) (Initiation factor 2- P50579 /1ETAP2 478 FALSE FALSE FALSE FALSE FALSE FALSE associated 67 kDa glycoprotein) (p67) (p67e!F2) (Peptidase M) Methionine-tRNA !igase, cytoplasmic (EC P56192 MARS 6.1 . 1 .10) (Methionyi-tRNA synthetase) 30 FALSE FALSE FALSE FALSE FALSE FALSE (MetRS) Methy!-CpG-binding domain protein 3 (Methy!- 095983 MBD3 1 FALSE FALSE FALSE TRUE FALSE FALSE CpG-binding protein MBD3) Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial (MCCase subunii alpha) (EC 6.4.1 .4) (3-methylcrotonyl-CoA Q96RQ3 MCCC1 carboxylase 1) (3-methylcrotonyl-CoA 725 FALSE FALSE FALSE FALSE FALSE FALSE carboxylase biotin-coniaining subunit) (3- methylcrotonyl-CoA:carbon dioxide ligase subunii alpha) Methylosome protein 50 (MEP-50) (Androgen Q9BQA1 WDR77 receptor cofactor p44) (WD repeat-containing FALSE FALSE FALSE TRUE FALSE FALSE protein 77) (p44/Mep50) Methylsterol monooxygenase 1 (EC Q15800 MSM01 293 TRUE FALSE FALSE TRUE FALSE TRUE 1.14.13.72) (C-4 methylsterol oxidase)

Q8N6R0 1ETTL1 3 Methyltransferase-like protein 13 (EC 2.1 . 1 .-) 699 FALSE FALSE FALSE FALSE FALSE FAL

Q6P1Q9 METTL2B Methyltransferase-like protein 2B (EC 2.1 . 1 .-) 378 FALSE FALSE FALSE FALSE FALSE TRUE

QQ3426 VK eva ona e kinase (MK) (EC 2.7. 1.36) 396 FALSE FALSE FALSE FALSE FALSE FALSE COS complex subunit MIC19 (Coiled-coil- Q9NX63 CHCHD3 helix-coiied-coil-helix domain-containing 227 FALSE FALSE FALSE TRUE TRUE TRUE protein 3) MICOS complex subunit MIC60 (Ceil proliferation-inducing gene 4/52 protein) Q16891 MMT 758 FALSE FALSE FALSE FALSE FALSE FALSE (Mitochondrial inner membrane protein) (Mitofilin) (p87/89) Microtubuie-actin cross-linking factor 1, isoforms 1/2/3/5 (620 kDa actin-binding Q9UPN3 7388 FALSE FALSE FALSE TRUE FALSE FALSE protein) (ABP620) (Actin cross-linking family protein 7) (Macrophin-1) (Trabecuiin-aipha)

P27816 Microtubule-associated protein 4 (MAP-4) 1152 FALSE FALSE FALSE TRUE FALSE TRUE Microtubule-associated protein RP/EB family 015691 MAPRE1 member 1 (APC-binding protein EB1) (End- 268 FALSE FALSE FALSE FALSE FALSE FALSE binding protein 1) (EB1) Microtubule-associated protein RP/EB family 015555 MAPRE2 member 2 (APC-binding protein EB2) (End- 327 FALSE TRUE FALSE TRUE TRUE TRUE binding protein 2) (EB2) Q9NU22 MDN1 Midasin (MIDAS-containing protein) 5596 TRUE FALSE TRUE FALSE FALSE FALSE Mirnitin, mitochondrial (B17.2-like) (B17.2L) (Myc-induced mitochondrial protein) (MMTN) Q8N183 NDUFAF2 (NADH dehydrogenase [ubiquinone] 1 alpha 169 FALSE FALSE FALSE FALSE FALSE FALSE subcomplex assembly factor 2) (NDUFA12- ike protein) Minor histocompatibility antigen H13 (EC 3.4.23.-) (Intramembrane protease 1) (IMP-1) Q8TCT9 HM13 377 FALSE FALSE FALSE TRUE TRUE TRUE (IMPAS-1) (WMP1) (Presenilin-like protein 3) (Signal peptide peptidase)

Mitochondrial antiviral-signaling protein (MAVS) (CARD adapter inducing interferon beta) (Cardif) (Interferon beta promoter Q7Z434 MAVS 540 FALSE FALSE FALSE FALSE FALSE TRUE stimulator protein 1) (!PS-1) (Putative NF- kappa~B-activating protein 031 ) (Virus- induced-signaling adapter) (VISA) Mitochondrial carrier homolog 1 (Preseniiin- Q9NZJ7 MTCH1 389 FALSE! FALSE FALSE FALSE FALSE FALSE associated protein) Mitochondrial carrier homolog 2 (Met-induced Q9Y6C9 MTCH2 3 3 FALSE! FA LSE FALSE TRUE TRUE TRUE mitochondrial protein) Mitochondrial chaperone BCS1 (h-BCS1) Q9Y276 BCS1 L 419 TRUE TRUE FALSE FALSE FALSE FALSE (BCS1-like protein) SLC25A1 Mitochondrial dicarboxyiate carrier (Solute Q9UBX3 287 TRUE TRUE FALSE FALSE FALSE FALSE 0 carrier family 25 member ) Mitochondrial import inner membrane trans!ocase subunit T 16 (Mitochondria- associated granulocyte macrophage CSF- Q9Y3D7 PAM16 125 TRUE FALSE FALSE FALSE FALSE FALSE signa!ing molecule) (Presequence translocated-associated motor subunit PA 16) Mitochondrial import inner membrane 060830 TIMM17B 172 TRUE FALSE FALSE FALSE TRUE FALSE translocase subunit Tim17-B Mitochondrial import inner membrane 043615 ΤΊ ΜΜ44 452 TRUE TRUE FALSE TRUE FALSE FALSE translocase subunit T M44 Mitochondrial import inner membrane Q3ZCQ8 TIMM50 353 FALSE FALSE FALSE FALSE FALSE FALSE translocase subunit TIM5Q Mitochondrial import receptor subunit TOM22 Q9NS69 TOMM22 homoiog (hTom22) (1C9-2) (Translocase of 142 FALSE FALSE FALSE TRUE TRUE TRUE outer membrane 22 kDa subunit homoiog) Mitochondrial import receptor subunit TOM34 Q15785 TOMM34 (hTom34) (Translocase of outer membrane 34 309 FALSE FALSE FALSE FALSE FALSE FALSE kDa subunit) Mitochondrial import receptor subunit TO 40 homoiog (Protein Haymaker) (Translocase of 096008 TOMM40 361 FALSE FALSE FALSE FALSE FALSE FALSE outer membrane 40 kDa subunit homoiog) (p38.5) Mitochondrial import receptor subunit TOM70 (Mitochondrial precursor proteins import 094826 TOMM70 receptor) (Transiocase of outer membrane 70 608 TRUE TRUE FALSE TRUE TRUE TRUE kDa subunit) (Translocase of outer mitochondrial membrane protein 70)

Mitochondrial Rho GTPase 1 (MIRO-1) (hMiro- 1) (EC 3 6.5.-) (Rac-GTP-binding protein-like Q8IXI2 RHOT1 618 FALSE FALSE FALSE TRUE FALSE TRUE protein) (Ras homoiog gene family member T1) Mitochondrial Rho GTPase 2 (MIRO-2) (hMiro- Q8IXM RHOT2 2) (EC 3 6.5.-) (Ras homoiog gene family 18 FALSE FALSE FALSE FALSE TRUE TRUE member T2) Mitochondrial ribonuciease P protein 1 (Mitochondrial RNase P protein 1) (EC 2.1 . 1 .-) (HBV pre-S2 trans-regulated protein 2) (RNA Q7L0Y3 TRMT10C (guanine-9-)-methyltransferase domain- 403 TRUE TRUE FALSE FALSE FALSE TRUE containing protein 1) (Renal carcinoma antigen NY-REN-49) (tRNA methyltransferase 10 homoiog C) Mitochondrial-processing peptidase subunit Q10713 P PCA 525 TRUE FALSE FALSE FALSE FALSE TRUE alpha (EC 3.4.24 64) (Alpha-MPP) (P-55)

Mitochondrial-processing peptidase subunit 075439 P PCB 489 TRUE TRUE FALSE FALSE FALSE FALSE beta (EC 3.4.24.64) (Beta-MPP) (P-52)

Mitogen-activated protein kinase 14 (MAP kinase 14) (MAPK 14) (EC 2.7.1 1 24) (Cytokine suppressive anti-inflammatory drug- binding protein) (CSAID-binding protein) Q16539 1APK14 360 FALSE FALSE FALSE FALSE FALSE FALSE (CSBP) (MAP kinase MXI2) (MAX-interacting protein 2) (Mitogen-activated protein kinase p38 alpha) (MAP kinase p38 alpha) (Stress- activated protein kinase 2a) (SAPK2a)

043684 BUBS Mitotic checkpoint protein BUB3 328 FALSE FALSE FALSE FALSE FALSE FALSE MKI67 FHA domain-interacting nucleolar phosphoprotein (Nucieoiar phosphoprotein 9 Q9BYG3 N!FK 293 TRUE TRUE FALSE FALSE FALSE FALSE Nopp34) (Nucleolar protein interacting with the FHA domain of pKI-67) (hNIFK) MMS19 nucleotide excision repair protein Q96T76 1S19 homoiog (hMMS19) (MET18 homoiog) 1030 FALSE FALSE FALSE TRUE FALSE FALSE (MMS19-like protein) MOB kinase activator 1B (Mob1 homoiog 1A) Q7L9L4 Ο Β1B (Mob1 A) (Mob1 B) (Mps one binder kinase 216 FALSE FALSE FALSE FALSE TRUE FALSE activator-like 1A) Moesin (Membrane-organizing extension P26038 MSN 577 FALSE FALSE FALSE FALSE FALSE FALSE spike protein) Monocarboxylate transporter 1 (MCT 1) P53985 SLC16A1 500 FALSE FALSE FALSE TRUE FALSE TRUE (Solute carrier family 16 member 1) Monofunctional C1-tetrahydrofolate synthase, Q6UB35 1THFD1 L mitochondrial (EC 6.3.4.3) 978 FALSE TRUE FALSE TRUE TRUE FALSE (Formyltetrahydrofolate synthetase) Mothers against decapentaplegic hornolog 2 (MAD hornolog 2) (Mothers against DPP Q 15796 SMAD2 homo!og 2) (JV18-1) (Mad-related protein 2) 467 TRUE TRUE FALSE FALSE FALSE TRUE (hMAD-2) (SMAD family member 2) (SMAD 2) (Smad2) (hSMAD2)

mRNA cap guanine-N7 methyltransferase (EC 2.1 . 1 .56) (RG7MT1) (mRNA (guanine-N(7)-)- 043148 476 FALSE FALSE FALSE FALSE FALSE FALSE meihyltransferase) (mRNA cap methyltransferase) (hCMT1) (hMet) (hcmlp)

mRNA export factor (Rae1 protein hornolog) RAE1 368 FALSE FALSE FALSE FALSE. FALSE (mRNA-associated protein mrnp 41)

mRNA turnover protein 4 hornolog (Ribosome Q9UKD2 1RT04 239 TRUE FALSE FALSE FALSE FALSE TRUE assembly factor MRT04) Multifunctional methyltransferase subunit Q9UI3Q TRMT1 12 T R 112-like protein (tRNA methyltransferase 125 FALSE FALSE FALSE FALSE FALSE TRUE 2 hornolog)

Multifunctional protein ADE2 [Includes: Phosphoribosyiaminoimidazole- succinocarboxamide synthase (EC 6.3.2.6) P22234 PAICS 425 FALSE FALSE FALSE FALSE FALSE FALSE (SAiCAR synthetase); Phosphoribosylaminoimidazole carboxylase (EC 4.1 . 1 .21) (AIR carboxylase) (AIRC)]

Multiple myeloma tumor-associated protein 2 Q9BU76 TAG2 263 FALSE FALSE FALSE FALSE FALSE FALSE (hMMTAG2) Musclebiind-like protein 1 (Triplet-expansion Q9NR56 V1BNL1 388 FALSE FALSE FALSE FALSE FALSE FALSE RNA-binding protein) 1YBBP1 Q9BQG0 Myb-binding protein 1A 1328 FALSE TRUE FALSE FALSE FALSE FALSE A Myeloid-associaied differentiation marker Q96S97 A D 322 FALSE FALSE FALSE FALSE FALSE FALSE (Protein SB135) Myeioid-derived growth factor (MYDGF) Q969H8 ^YDGF (interleukin-25) (IL-25) (Stromal cell-derived 173 TRUE FALSE FALSE TRUE FALSE FALSE growth factor SF20) Myosin regulatory light chain 12B (MLC-2A) (MLC-2) (Myosin regulatory light chain 2-B, 014950 MYL12B smooth muscle isoform) (Myosin regulatory 172 FALSE FALSE FALSE FALSE FALSE FALSE light chain 20 kDa) (MLC2Q) (Myosin regulatory light chain MRLC2) (SHUJUN-1)

Myosin-10 (Cellular myosin heavy chain, type B) (Myosin heavy chain 10) (Myosin heavy chain, non-muscle lib) (Non-muscle myosin P35580 1YH10 1976 FALSE FALSE FALSE FALSE FALSE FALSE heavy chain B) (NMMHC-B) (Non-muscle myosin heavy chain l b) (NMMHC ll-b) ( MMHC- B) Myosin-9 (Cellular myosin heavy chain, type A) (Myosin heavy chain 9) (Myosin heavy chain, non-muscle Ma) (Non-muscle myosin P35579 3YH9 1960 FALSE FALSE FALSE! FALSE FALSE FALSE heavy chain A) (NMMHC-A) (Non-muscle myosin heavy chain a) (NMMHC M-a) (NMMHC-MA) P58546 T PN Myotrophin (Protein V-1) 118 FALSE FALSE FALSE FALSE FALSE FALSE Myotubularin-related protein 14 (EC 3.1 .3.-) (HCV NS5A-transactivated protein 4 splice Q8NCE2 T 650 FALSE FALSE FALSE FALSE FALSE FALSE variant A-binding protein 1) (NS5ATP4ABP1) (hJumpy) N-acyineuraminate cytidyiyltransferase (EC Q8NFW8 CMAS 2.7.7.43) (CMP-N-acetylneuraminic acid 434 FALSE FALSE FALSE FALSE TRUE TRUE synthase) (CMP-NeuNAc synthase) N-alpha-acetyltransferase 10 (EC 2.3.1 255) (N-terminal acetyltransferase complex ARD1 P41227 NAA10 235 FALSE FALSE FALSE FALSE FALSE FALSE subunit homolog A) (NatA catalytic subunit Naa10) N-alpha-acetyltransferase 15, NatA auxiliary subunit (Gastric cancer antigen Ga19) (N- Q9BXJ9 NAA15 terminal acetyltransferase) (NMDA receptor- 866 FALSE FALSE FALSE TRUE FALSE FALSE regulated protein 1) (Protein tubedown-1) (TbdnlOO) N-alpha-aceiyltransferase 50 (EC 2.3.1 258) (N-acetyltransferase 13) (N-aceiyltransferase Q9GZZ1 NAA50 169 FALSE FALSE FALSE TRUE TRUE FALSE 5) (hNAT5) (N-aceiyltransferase san homoiog) (hSAN) (NatE catalytic subunii)

N-terminal Xaa-Pro~Lys N~methyltransferase 1 (EC 2.1 . 1 .244) (Alpha N-terminal protein methyltransferase 1 ) (Methyltransferase-like protein 11A) (N-terminal RCC1 Q9BV86 NTMT1 223 FALSE FALSE FALSE FALSE FALSE FALSE methyltransferase) (X-Pro-Lys N-terminal protein methyltransferase 1A) (NTM1A) [Cleaved into: N-terminal Xaa-Pro-Lys N- methyltransferase 1, N~terminally processed]

NAD kinase 2 , mitochondrial (EC 2.7.1 .23)

Q4G0N4 NADK2 (Mitochondrial NAD kinase) (NAD kinase F L3 Ε A L Ξ F L3 Ε F LS Ε FA L Ξ FA L3 EE domain-containing protein 1, mitochondrial)

NAD-dependent malic enzyme, mitochondrial P23368 ME2 584 FALSE FALSE FALSE FALSE FALSE FALSE (NAD-ME) (EC 1. 1 . 1 .38) (Malic enzyme 2)

NAD(P) transhydrogenase, mitochondrial (EC 1.6.1 .2) (Nicotinamide nucleotide Q13423 NNT 1086 FALSE FALSE FALSE FALSE FALSE FALSE transhydrogenase) (Pyridine nucleotide transhydrogenase)

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Q95299 NDUFA10 355 TRUE FALSE FALSE TRUE FALSE FALSE (Complex l-42kD) (Ci-42kD) (NADH- ubiquinone oxidoreductase 42 kDa subunit)

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (Complex 1-B8) (CI-B8) 043678 NDUFA2 FALSE FALSE FALSE FALSE FALSE FALSE (NADH-ubiquinone oxidoreductase B8 subunit) NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (Complex subunit B 13) Q 1671 8 16 FALSE FALSE FALSE FALSE FALSE FALSE (Complex !~ 3kD~B) (CI-1 3kD-B) (NADH- ubiquinone oxidoreduciase 3 kDa-B subunit)

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9 , mitochondrial Q 6795 NDUFA9 377 FALSE FALSE FALSE FALSE FALSE FALSE (Complex l-39kD) (CI-39kD) (NADH- ubiquinone oxidoreductase 39 kDa subunit)

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (Complex I-B1 5) (C - 0951 68 NDUFB4 129 FALSE FALSE FALSE FALSE FALSE FALSE B 15) (NADH-ubiquinone oxidoreductase B 15 subunit)

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 , mitochondrial (EC 1.6.5.3) (EC 075306 NDUFS2 463 TRUE FALSE FALSE FALSE TRUE FALSE 1.6.99.3) (Complex l-49kD) (CI-49kD) (NADH- -4 ubiquinone oxidoreductase 49 kDa subunit)

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 , mitochondrial (EC 1.6.5.3) (EC 075489 NDUFS3 264 FALSE TRUE FALSE FALSE FALSE FALSE 1.6.99.3) (Complex l-30kD) (CI-30kD) (NADH- ubiquinone oxidoreductase 30 kDa subunit)

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 , mitochondrial (EC 1 6.5.3) (EC 0002 17 NDUFS8 1.6.99.3) (Complex l-23kD) (CI-23kD) (NADH- 210 FALSE TRUE FALSE FALSE FALSE FALSE ubiquinone oxidoreductase 23 kDa subunit) (TYKY subunit) NADH-cytochrome b5 reductase 3 (B5R) (Cytochrome b5 reductase) (EC 1.6.2.2) (Diaphorase-1 ) [Cleaved into: NADH- 7 CYB5R3 301 FALSE FALSE FALSE FALSE FALSE FALSE cytochrome b5 reductase 3 membrane-bound form; NADH-cytochrome b5 reductase 3 soluble form] NADH-ubiquinone oxidoreductase 75 kDa P28331 NDUFS1 subunit, mitochondrial (EC 1.6.5 3) (EC 727 FALSE TRUE FALSE FALSE TRUE FALSE 1.6.99.3) (Complex l-75kD) (CI-75kD) NADH-ubiquinone oxidoreductase chain 4 (EC P03905 T- D4 459 FALSE FALSE FALSE FALSE FALSE FALSE 1.6.5.3) (NADH dehydrogenase subunit 4)

NADH-ubiquinone oxidoreductase chain 5 (EC P03915 T- 5 603 FALSE FALSE FALSE FALSE FALSE FALSE 1.6.5.3) (NADH dehydrogenase subunit 5)

NADPH-cytochrome P45Q reductase (CPR) P16435 POR 677 FALSE FALSE! FALSE FALSE FA LS (P450R) (EC 1.6.2.4) Nardilysin (EC 3.4.24.61) (N-arginine dibasic 043847 NRDC convertase) (NRD convertase) (NRD-C) 1150 FALSE FALSE FALSE TRUE FALSE FALSE (Nardilysin convertase)

Nascent poiypeptide-associated complex E9PAV3 NACA subunit alpha, muscle-specific form (Aipha- 2078 FALSE FALSE L FALSE FALSE FALSE NAC, muscle-specific form) (skNAC)

NEDD8~activating enzyme E 1 regulatory subunit (Amyloid beta precursor protein- Q 13564 NAE1 binding protein 1, 59 kDa) (APP-BP1) 534 FALSE FALSE FALSE FALSE FALSE FALSE (Amyloid protein-binding protein 1) (Proto- oncogene protein 1)

NEDDS-conjugating enzyme Ubc12 (EC 6.3.2.- UBE2I* ) (NEDD8 carrier protein) (NEDD8 protein 183 FALSE FALSE FALSE FALSE TRUE TRUE ligase) (Ubiquitin-conjugating enzyme E2 M)

Negative elongation factor B (NELF-B) Q8WX92 NELFB 580 FALSE FALSE FALSE FALSE FALSE FALSE (Cofactor of BRCA1) Negative elongation factor E (NELF-E) (RNA- P18615 NELFE 380 FALSE FALSE FALSE FALSE FALSE FALSE binding protein RD)

Neurabin-2 (Neurabin-ll) (Protein phosphatase Q96SB3 PPP1 R9B 815 FALSE FALSE FALSE 1 regulatory subunit 9B) (Spinophilin)

Neuroblastoma-amplified sequence A2RRP1 NBAS 2371 FALSE TRUE FALSE FALSE FALSE FALSE (Neuroblastoma-ampiified gene protein) Neuroiysin, mitochondrial (EC 3 4.24.16) (Angiotensin-binding protein) (Microsomal Q9BYT8 NLN endopeptidase) (MEP) (Mitochondrial 704 FALSE FALSE FALSE FALSE FALSE FALSE oligopeptidase M) (Neurotensin endopeptidase) Neutral alpha-glucosidase AB (EC 3 2.1.84) Q14697 GANAB (Alpha-glucosidase 2) (Giucosidase subunit 944 FALSE FALSE FALSE FALSE FALSE FALSE alpha) Q8NBF2 NHLRC2 NHL repeat-containing protein 2 726 FALSE FALSE FALSE FALSE FALSE FALSE

NHP2~like protein 1 (High mobility group-like nuclear protein 2 homolog 1) (OTK27) (SNU13 homolog) (hSNU13) (U4/U6.U5 small P55769 SNU13 128 TRUE TRUE TRUE FALSE FALSE FALSE nuclear ribonucleoprotein SNU13) (U4/U6.U5 tri-snRNP 15.5 kDa protein) [Cleaved into: NHP2-like protein 1, N-terminally processed]

Q969V3 NCLN Nicalin (Nicastrin-like protein) 563 FALSE TRUE FALSE TRUE TRUE FALSE Nicotinamide phosphonbosyltransferase (NAmPRTase) (Nampt) (EC 2 4.2.12) (Pre-B- P43490 NAMPT 491 FALSE FALSE FALSE FALSE FALSE FALSE ce colony-enhancing factor 1) (Pre-B cell- enhancing factor) (Visfatin) Nipped-B-like protein (Delangin) (SCC2 Q6KC79 N PBL 2804 FALSE FALSE FALSE TRUE TRUE FALSE homolog) Nitric oxide synthase-interacting protein (E3 ubiquifin-protein ligase NOSIP) (EC 2 3.2.27) Q9Y314 NOSIP 301 TRUE TRUE TRUE TRUE TRUE TRUE (RING-type E3 ubiquitin transferase NOSIP) (eNOS-interacting protein)

Non-histone chromosomal protein HMG-14 P051 4 H GN1 (High mobility group nucleosome-binding FALSE FALSE FALSE FALSE FALSE FALSE domain-containing protein 1) Non-histone chromosomal protein HMG-17 P05204 H GN2 (High mobility group nucleosome-binding 90 FALSE FALSE FALSE FALSE FALSE FALSE domain-containing protein 2) Non-POU domain-containing octamer-binding protein (NonO protein) (54 kDa nuclear RNA- Q15233 NONO and DNA-binding protein) (55 kDa nuclear 471 FALSE FALSE FALSE FALSE FALSE FALSE protein) (DNA-binding p52/p100 complex, 52 kDa subunit) (N T55) (p54(nrb)) (p54nrb)

Non-specific lipid-transfer protein (NSL-TP) (EC 2.3.1 .176) (Propanoyl-CoA C- P223Q7 SCP2 acyltransferase) (SCP-chi) (SCPX) (Sterol 547 FALSE TRUE FALSE FALSE TRUE TRUE carrier protein 2) (SCP-2) (Sterol carrier protein X) (SCP-X) Q9NVX2 NLE1 Notchless protein homolog 1 485 FALSE FALSE TRUE FALSE FA FALSE NSFL1 cofactor p47 (UBX domain-containing Q9UNZ2 NSFL1C 370 FALSE FALSE FALSE FALSE FALSE FALSE protein 2C) (p97 cofactor p47)

P49321 NASP Nuclear autoantigenic sperm protein (NASP) 788 F S ! FALSE FA F S FALSE FALSE

Nuclear cap-binding protein subunit 1 (80 kDa QQ9161 NCBP1 nuclear cap-binding protein) (CBP80) (NCBP 790 FALSE FALSE FALSE TRUE FALSE TRUE -4 80 kDa subunit)

Nuclear inhibitor of protein phosphatase 1 (N!PP-1) (Protein phosphatase 1 regulatory Q12972 PPP1 R8 351 FALSE FALSE FALSE FALSE FALSE FALSE inhibitor subunit 8) [includes: Activator of RNA decay (EC 3.1 .4.-) (ARD-1)] Nuclear migration protein nudC (Nuclear Q9Y266 NUDC 331 FALSE FALSE FALSE FALSE FALSE FA.LSE distribution protein C homolog) Nuclear mitotic apparatus protein 1 (Nuclear matrix protein-22) (NMP-22) (Nuclear mitotic Q14980 NU A 1 2 115 FALSE FALSE FALSE FALSE FALSE FALSE apparatus protein) (NuMA protein) (SP-H antigen)

Nuclear pore complex protein Nup107 (107 P57740 NUP107 2 5 TRUE TRUE TRUE TRUE FALSE FALSE kDa nucleoporin) (Nucleoporin Nup107)

Nuclear pore complex protein Nup133 (133 Q8W U 0 NUP133 1156 TRUE TRUE TRUE FALSE FALSE FALSE kDa nucleoporin) (Nucleoporin Nup133) Nuclear pore complex protein Nup1 53 ( 53 P49790 NUP1 53 1475 TRUE FALSE TRUE TRUE TRUE TRUE kDa nucleoporin) (Nucleoporin Nup1 3)

Nuclear pore complex protein Nup1 55 ( 55 075694 NUP1 55 1391 TRUE TRUE TRU E FALSE FALSE FALSE kDa nucleoporin) (Nucleoporin Nup1 55)

NLfdear pore complex protein Nup1 60 ( 160 Q 12769 NUP1 6 Q 1436 FALSE TRUE TRUE FALSE TRUE FALSE kDa nucleoporin) (Nucleoporin NLfp1 60)

Nuclear pore complex protein Nup205 (205 Q92621 NUP205 2 12 FALSE FALSE FALSE FALSE FALSE FALSE kDa nucleoporin) (Nucleoporin Nup205)

Nuclear pore complex protein Nup2 14 (2 4 P35658 NUP2 14 kDa nucleoporin) (Nucleoporin Nup2 14) 2090 FALSE FALSE FALSE TRU E FALSE FALSE (Protein CAN)

Nuclear pore complex protein Nup50 (50 kDa Q9UKX7 NUP50 nucleoporin) (Nuclear pore-associated protein 468 FALSE FALSE FALSE FALSE FALSE FALSE 60 kDa-like) (NLideoporin Nup50)

Nuclear pore complex protein Nup85 (85 kDa Q9BW27 NUP85 nucleoporin) (FROUNT) (Nucleoporin Nup75) 656 TRUE TRUE FALSE TRUE TRUE FALSE (Nucleoporin Nup85) (Pericentrin-1 )

Nuclear pore complex protein Nup88 (88 kDa Q99567 NUP88 741 TRUE TRUE TRUE TRUE TRUE FALSE nucleoporin) (Nucleoporin Nup88) Nuclear pore complex protein Nup93 (93 kDa Q8N 1F7 NUP93 8 19 FALSE FALSE FALSE FALSE FALSE FALSE nucleoporin) (Nucleoporin Nup93)

Nuclear pore complex protein Nup98-Nup96 (EC 3.4.2 1.-) [Cleaved into: Nuclear pore complex protein Nup98 (98 kDa nucleoporin) P52948 NUP98 18 17 FALSE FALSE! FALSE FALSE FALSE (Nucleoporin Nup98) (Nup98); Nuclear pore complex protein Nup96 (96 kDa nucleoporin) (Nucleoporin Nup96) (Nup96)]

Nuclear pore glycoprotein p62 (62 kDa P371 98 NUP62 522 TRUE FALSE FALSE FALSE TRUE FALSE nucleoporin) (Nucleoporin Nup62) Nuclear pore membrane glycoprotein 210 (Nuclear pore protein gp210) (Nuclear Q8TEM1 NUP210 envelope pore membrane protein POM 210) 1887 FALSE FALSE FALSE FALSE FALSE FALSE (POM210) (Nucleoporin Nup210) (Pore membrane protein of 2 kDa) Nuclear protein localization protein 4 homolog Q8TAT6 NPLOC4 608 FALSE FALSE FALSE FALSE FALSE FALSE (Protein NPL4) Q9UHY1 NRBP1 Nuclear receptor-binding protein 535 FALSE FALSE FALSE FALSE FALSE FALSE Nuclear RNA export factor 1 (Tip-associated Q9UBU9 NXF1 protein) (Tip-associating protein) (mRNA 619 FALSE TRUE FALSE FALSE FALSE FALSE export factor TAP) Nuclear valosin-containing protein-like (NVLp) 015381 NVL 856 FALSE TRUE FALSE FALSE FALSE TRUE (Nuclear VCP-like protein) Nuclease-sensitive element-binding protein 1 (CCAAT-binding transcription factor I subunit A) (CBF-A) (DNA-binding protein B) (DBPB) P67809 YBX1 324 FALSE FALSE FALSE FALSE FALSE FALSE (Enhancer factor subunit A) (EFI-A) (Y-box transcription factor) (Y-box~binding protein 1) -4 •J\ (YB-1)

Nucleolar and coiled-body phosphoprotein 1 (140 kDa nucleolar phosphoprotein) (Nopp140) (Hepatitis C virus NS5A- Q14978 NOLC1 699 FALSE FALSE FALSE FALSE FALSE FALSE transactivated protein 13) (HCV NS5A- transactivated protein 13) (Nucleolar 130 kDa protein) (Nucleolar phosphoprotein p130) Nucleolar complex protein 2 homolog (Protein Q9Y3T9 NOC2L NOC2 homolog) (NOC2-like protein) (Novel 9 TRUE TRUE TRUE FALSE FALSE FALSE HAT repressor) Nucleolar complex protein 3 homolog (NOC3 protein homolog) (Factor for adipocyte Q8WTT2 NOC3L differentiation 24) (NOC3-like protein) 800 TRUE TRUE FALSE FALSE FALSE FALSE (Nucleolar complex-associated protein 3-like protein) Nucleolar complex protein 4 homolog (NOC4 protein homolog) (NOC4-like protein) Q9BVI4 NOC4L 516 TRUE TRUE TRUE FALSE FALSE FALSE (Nucleolar complex-associated protein 4-like protein) Nucleolar GTP-binding protein 1 (Chronic Q9BZE4 GTPBP4 renal failure gene protein) (GTP-binding 634 FALSE FALSE FALSE FALSE FALSE FALSE protein NGB) Nucleolar F4G domain-containing protein 1 Q5C9Z4 NO 1 860 FALSE FALSE FALSE FALSE TRUE FALSE (SGD1 homolog) Nucleolar pre-ribosoma!-associated protein 1 060287 URB1 (Nucleolar protein 254 kDa) (URB1 ribosome 2271 FALSE FALSE FALSE FALSE FALSE FALSE biogenesis 1 homolog) Q9BSC4 NOL10 Nucleolar protein 10 688 TRUE FALSE FALSE FALSE FALSE TRUE Q9H8H0 NOL1 1 Nucleolar protein 11 719 FALSE FALSE FALSE FALSE FA LS FALSE Nucleolar protein 16 (HBV pre-S2 trans- Q9Y3C1 NOP16 178 F S ! F FA L F LS FALSE FALSE regulated protein 3) OQ0567 NOP56 Nucleolar protein 56 (Nucleolar protein 5A) 594 FALSE FALSE FALSE TRUE TRUE TRUE Q9Y2X3 NOP58 Nucleolar protein 58 (Nucleolar protein 5) 529 FALSE FALSE FALSE FALSE FALSE FALSE Nucleolar protein 6 (Nucleolar RNA- Q9H6R4 NOL6 1146 TRUE TRUE TRUE FALSE FALSE FALSE associated protein) (Nrap) Nucleolar RNA helicase 2 (EC 3.6.4.13) (DEAD box protein 21) (Gu-aipha) (Nucleolar Q9NR30 DDX21 783 FALSE FALSE FA L FA L FALSE FALSE RNA helicase Gu) (Nucleolar RNA helicase II) (RH ll/Gu)

Nucleolar transcription factor 1 (Autoantigen P17480 UBTF 764 TRUE TRUE TRUE FALSE TRUE TRUE NOR-90) (Upstream-binding factor 1) (UBF-1)

P19338 NCL Nucleolin (Protein C23) 710 FALSE FALSE FALSE FALSE FALSE FALSE Q01085 TIAL1 Nucleoiysin T A R (TIA-1 -related protein) 375 FALSE TRUE FALSE FALSE FALSE FALSE Nucleophosmin (NPM) (Nucleolar P06748 NP 1 phosphoprotein B23) (Nucleolar protein N038) 294 FALSE FALSE FALSE FALSE FALSE FALSE (Numatrin) 075607 NP 3 Nucieopiasmin-3 178 FALSE FALSE FALSE TRUE FALSE FALSE Nucleoporin NDC1 (hNDC1) (Transmembrane Q9BTX1 NDC1 674 FALSE TRUE TRUE FALSE FALSE TRUE protein 48) Q5SRE5 NUP188 Nucleoporin NUP188 homolog (hNup188) 1749 TRUE FALSE! TRUE TRUE TRUE TRUE N c eopo n Nup37 (p37) (Nup107-180 Q8NFH4 NUP37 326 FALSE FALSE FALSE TRUE TRUE TRUE subcomplex subunit Nup37) Nucleoporin Nup43 (Nup107-160 subcomplex Q8NFH3 NUP43 380 FALSE FALSE FALSE TRUE TRUE TRUE subunit Nup43) (p42) Q7Z3B4 NUP54 Nucleoporin p54 (54 kDa nucleoporin) 507 FALSE FALSE FALSE FALSE FALSE FALSE Nucleoporin SEH1 (GATOR complex protein Q96EE3 SEH1 L SEH1) (Nup107-160 subcomplex subunit 360 FALSE FALSE FALSE TRUE TRUE TRUE SEH1) (SEC13-iike protein) Nucleoprotein TPR (Megator) (NPC- P12270 TPR associated intranuclear protein) (Translocated 2363 FALSE FALSE FALSE TRUE TRUE TRUE promoter region protein) Nucleoside diphosphate kinase A (NDK A) (NDP kinase A) (EC 2.7.4.6) (Granzyme A- P15531 N E1 activated DNase) (GAAD) (Metastasis 152 FALSE FALSE FALSE FALSE FALSE FALSE inhibition factor nm23) (NM23-H1) (Tumor metastatic process-associated protein) Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (C-myc purine- -4 -4 P22392 N E2 binding transcription factor PUF) (Histidine 152 FALSE FALSE FALSE FALSE FALSE FALSE protein kinase NDKB) (EC 2.7.13.3) (nm23- H2) Nudeosome assembly protein 1-like 1 (NAP-1 P55209 NAP1L1 391 FALSE TRUE TRUE TRUE related protein) (hNRP) S F . 3 E Nudeosome assembly protein 1-like 4 Q99733 NAP1L4 375 TRUE FALSE FALSE FALSE FALSE FALSE (Nudeosome assembly protein 2) (NAP-2)

Q8WVJ2 NUDCD2 NudC domain-containing protein 2 157 FALSE FALSE FALSE FALSE TRUE TRUE O-acetyl-ADP-ribose deacetyiase 1 (EC 3 5.1. Q9Y530 OARD1 152 TRUE TRUE FALSE FALSE FALSE FALSE ) Obg-like ATPase 1 (DNA damage-regulated Q9NTK5 OLA1 overexpressed in cancer 45) (DOC45) (GTP- 396 FALSE FALSE FALSE TRUE TRUE TRUE binding protein 9) OC A domain-containing protein 1 (Ovarian Q9NX40 OCIAD1 245 FALSE FALSE FALSE FALSE FALSE FALSE carcinoma immunoreactive antigen) Oligosaccharyltransferase complex subunit Q9NRP0 OSTC 149 FALSE FALSE FALSE FALSE FALSE FALSE OSTC (Hydrophobic protein HSF-28)

Opioid growth factor receptor (OGFr) (Protein Q9NZT2 OGFR 677 FALSE FALSE FALSE FALSE TRUE TRUE 7-60) (Zeta-type opioid receptor)

Origin recognition complex subunit 3 (Origin Q9UBD5 ORC3 7 11 FALSE TRUE FALSE TRUE TRUE FALSE recognition complex subunit Latheo)

043913 ORC5 Origin recognition complex subunit 5 435 FALSE FALSE FALSE FALSE FALSE FALSE OTU domain-containing protein 6B (EC Q8N6 0 OTUD6B 293 TRUE TRUE TRUE FALSE FALSE FALSE 3.4.19.12) (DUBA-5) P22059 OSBP Oxysterol-binding protein 1 807 FALSE FALSE FALSE TRUE TRUE TRUE Oxysterol-binding protein-related protein 8 Q9BZF1 OSBPL8 889 FALSE FALSE FALSE TRUE TRUE TRUE (ORP-8) (OSBP-related protein 8) p21 -activated protein kinase-interacting protein 1 (PAK/PLC-interacting protein 1) Q9NWT1 PAK1 IP1 392 FALSE FALSE! FALSE FALSE FALSE (hPIP1) (PAK1 -interacting protein 1) (WD repeat-containing protein 84) -4 Pachytene checkpoint protein 2 homo!og (Human papillomavirus type 16 E 1 protein- binding protein) (16E1-BP) (HPV16 E 1 protein- Q 15645 TRIP13 binding protein) (Thyroid hormone receptor 432 FALSE TRUE FALSE TRUE TRUE TRUE interactor 13) (Thyroid receptor-interacting protein 13) (TR-interacting protein 13) (TRIP- 13)

Paired amphipathic helix protein Sin3a Q96ST3 S 3A (Histone deacetylase complex subunit Sin3a) 1273 FALSE FALSE FALSE FALSE FALSE FALSE (Transcriptional corepressor SinSa)

Palmitoyl-protein thioesterase 1 (PPT-1) (EC P50897 PPT1 306 FALSE FALSE FALSE TRUE FALSE FALSE 3.1 .2.22) (Palmitoyl-protein hydrolase 1)

Parafibromin (Cell division cycle protein 73 Q6P1J9 CDC73 531 FALSE TRUE FALSE FALSE FALSE FALSE homolog) (Hyperparathyroidism 2 protein) Paraspeckle component 1 (Paraspeckle Q8WXF1 PSPC1 523 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) Partner of Y14 and ago (PYM homolog 1 Q9BRP8 PY 1 exon junction complex-associated factor) 204 FALSE FALSE FALSE FALSE FALSE FALSE (Protein wibg homolog) PC4 and SFRS1 -interacting protein (CLL- associated antigen KW-7) (Dense fine 075475 PSIP1 speckles 70 kDa protein) (DFS 70) (Lens 530 TRUE TRUE FALSE TRUE FALSE TRUE epithelium-derived growth factor) (Transcriptional coactivator p75/p52) Pentatricopeptide repeat domain-containing protein 3 , mitochondrial (28S ribosomal protein S39, mitochondrial) (MRP-S39) Q96EY7 PTCD3 689 FALSE FALSE! FALSE FALSE FA LS (Mitochondrial small ribosomal subunit protein mS39) (Transformation-related gene 5 protein) (TRG-15)

Peptidyl-prolyl cis-trans isomerase A (PPIase -4 A) (EC 5.2.1 .8) (Cyclophiiin A) (Cyclosporin A - P62937 PP A binding protein) (Rotamase A) [Cleaved into: 165 FALSE FALSE L FALSE FALSE FALSE Peptidyl-prolyl cis-trans isomerase A , ~ terminally processed]

Peptidyl-prolyl cis-trans isomerase B (PPIase P23284 PP B B) (EC 5.2.1 .8) (CYP-S1) (Cyclophiiin B) 216 FALSE FALSE FALSE FALSE FALSE FALSE (Rotamase B) (S-cyciophilin) (SCYLP)

Peptidyl-prolyl cis-trans isomerase D (PPIase D) (EC 5.2 1.8) (40 kDa peptidyl-prolyl cis- Q08752 PP D 370 TRUE FALSE FALSE FALSE FALSE TRUE trans isomerase) (Cyclophiiin-40) (CYP-40) (Cyciophilin-reiated protein) (Rotamase D)

Peptidyl-prolyl cis-trans isomerase F, mitochondrial (PPIase F) (EC 5.2.1 .8) P30405 PP!F (Cyclophiiin D) (CyP-D) (CypD) (Cyclophiiin F) 207 FALSE FALSE FALSE TRUE TRUE TRUE (Mitochondrial cyclophiiin) (CyP-M) (Rotamase F) Peptidyl-proiyl cis-trans isomerase FKBP2 (PPIase FKBP2) (EC 5.2.1 .8) (13 kDa FK506- P26885 FKBP2 binding protein) (13 kDa FKBP) (FKBP-1 3) 142 TRUE FALSE FALSE TRUE FALSE FALSE (FK506-binding protein 2) (FKBP-2) (Immunophilin FKBP13) (Rotamase)

Peptidyl-proiyl cis-trans isomerase FKBP3 (PPiase FKBP3) (EC 5.2.1 .8) (25 kDa FK506- binding protein) (25 kDa FKBP) (FKBP-25) 224 FALSE FALSE FALSE FALSE FALSE FALSE (FK506-binding protein 3) (FKBP-3) (immunophilin FKBP25) (Rapamycin-selective 25 kDa immunophilin) (Rotamase)

Peptidyl-proiyl cis-trans isomerase FKBP4 (PPiase FKBP4) (EC 5.2.1 .8) (51 kDa FK506- binding protein) (FKBP51) (52 kDa FK5Q6- binding protein) (52 kDa FKBP) (FKBP-52) (59 kDa immunophilin) (p59) (FK506-binding 459 FALSE FALSE FALSE FALSE FALSE FALSE protein 4) (FKBP-4) (FKBP59) (HSP-binding immunophilin) (HB ) (Immunophilin FKBP52) (Rotamase) [Cleaved into: Peptidyl-proiyl cis- trans isomerase FKBP4, N-terminaliy processed]

Peptidyl-proiyl cis-trans isomerase FKBP5 (PPiase FKBP5) (EC 5.2.1 .8) (51 kDa FK506- binding protein) (51 kDa FKBP) (FKBP-51) (54 kDa progesterone receptor-associated 457 FALSE FALSE FALSE FALSE TRUE TRUE immunophilin) (Androgen-regulated protein 6) (FF1 antigen) (FK506-binding protein 5) (FKBP-5) (FKBP54) (p54) (HSP90-binding immunophilin) (Rotamase) Peptidyl-proiyl cis-trans isomerase FKBP8 (PPIase FKBP8) (EC 5.2.1 .8) (38 kDa FK506- Q14318 FKBP8 binding protein) (38 kDa FKBP) (FKBP-38) 412 FALSE FALSE FALSE TRUE TRUE TRUE (hFKBP38) (FK506-binding protein 8) (FKBP- 8) (FKBPR38) (Rotamase) Peptidyl-proiyl cis-trans isomerase G (PPIase G) (Peptidyl-proiyl isomerase G) (EC 5.2.1.8) (CASP10) (Cik-associating RS-cyclophilin) Q13427 PP!G 754 FALSE FALSE FALSE FALSE TRUE TRUE (CARS-Cyp) (CARS-cyclophilin) (SR- cyclophilin) (SR-cyp) (SRcyp) (Cyclophiiin G) (Rotamase G)

Peptidyl-proiyl cis-trans isomerase H (PPIase H) (EC 5.2.1 .8) (Rotamase H) (Small nuclear 043447 PP H ribonucleoprotein particle-specific cyclophiiin 177 FALSE FALSE FALSE TRUE TRUE TRUE H) (CypH) (U-snRNP-associated cyclophiiin SnuCyp-20) (USA-CYP) Peptidyl-proiyl cis-trans isomerase NIMA- interacting 1 (EC 5.2.1 .8) (Peptidyl-proiyl cis- Q13526 PIN1 163 FALSE FALSE FALSE FALSE FALSE FALSE trans isomerase Pin1) (PPIase Pin1) (Rotamase Pin1) Peptidyl-proiyl cis-trans isomerase-like 1 Q9Y3C6 PPIL1 166 FALSE FALSE FALSE TRUE TRUE FALSE (PPIase) (EC 5.2.1 .8) (Rotamase PPIL1) Peptidyl-proiyl cis-trans isomerase-like 2 (PPIase) (EC 2.3.2.27) (EC 5.2.1.8) (CYC4) (Cyclophilin-60) (Cyclophilin-like protein Cyp- Q13356 PPIL2 520 FALSE FALSE FALSE FALSE FALSE FALSE 60) (Cyp60) (hCyP-60) (R G-type E3 ubiquitin transferase isomerase-like 2) (Rotamase PPIL2) Peptidyl-proiyl cis-trans isomerase-like 4 Q8WUA2 PPIL4 (PPIase) (EC 5.2.1 .8) (Cyclophilin-like protein 492 TRUE FALSE FALSE TRUE FALSE FALSE PPIL4) (Rotamase PPIL4) Peptidyi-tRNA hydrolase 2 , mitochondrial Q9Y3E5 PTRH2 (PTH 2) (EC 3 .1.1.29) (Bcl-2 inhibitor of 179 FALSE FALSE FALSE TRUE TRUE TRUE transcription 1) Pepiidylprolyl isomerase domain and W D Q96BP3 PPWD1 repeat-containing protein 1 (EC 5 2.1.8) 646 FALSE FALSE FALSE FALSE FALSE FALSE (Sp!iceosome-associated cyclophilin) Pericentriolar material 1 protein (PCM-1) Q15154 PCM1 2024 FALSE FALSE FALSE FALSE FALSE TRUE (hPCM-1) Perilipin-3 (47 kDa mannose 6-phosphate receptor-binding protein) (47 kDa MPR- binding protein) (Cargo selection protein 060664 PLIN3 434 FALSE FALSE FALSE FALSE FALSE FALSE TIP47) (Mannose-6-pbospbate receptor- binding protein 1) (Placental protein 1 ) (PP17) Q15269 PWP2 Periodic tryptophan protein 2 homolog 919 FALSE FALSE FALSE FALSE FALSE FALSE

Peroxiredoxin-1 (EC 1. 1 1.1 .15) (Natural killer cell-enhancing factor A) (NKEF-A) Q06830 PRDX1 (Proliferation-associated gene protein) (PAG) 199 FALSE FALSE FALSE FALSE FALSE FALSE (Thioredoxin peroxidase 2) (Thioredoxin- dependent peroxide reductase 2)

Peroxiredoxin-2 (EC 1. 1 1.1 .15) (Naiural killer cell-enhancing factor B) (NKEF-B) (PRP) P321 19 PRDX2 (Thiol-specific antioxidant protein) (TSA) 198 FALSE FALSE FALSE FALSE FALSE FALSE (Thioredoxin peroxidase 1) (Thioredoxin- dependent peroxide reductase 1)

Peroxiredoxin-4 (EC 1. 1 1.1 .15) (Antioxidant enzyme AOE372) (AOE37-2) (Peroxiredoxin Q13162 PRDX4 IV) (Prx-IV) (Thioredoxin peroxidase A0372) 271 FALSE FALSE FALSE FALSE FALSE FALSE (Thioredoxin-dependent peroxide reductase A0372) Peroxiredoxin-5, mitochondrial (EC 1. . 1 .15) (A u corepressor 1) (Antioxidant enzyme B166) (AOEB166) (Liver tissue 2D-page spot P30044 PRDX5 7 1B) (PLP) (Peroxiredoxin V) (Prx-V) 214 FALSE FALSE FALSE TRUE TRUE TRUE (Peroxisomal antioxidant enzyme) (TPx type Vi) (Thioredoxin peroxidase P P20) (Thioredoxin reductase)

Peroxiredoxin-6 (EC 1. 1 1.1 .15) (1-Cys peroxiredoxin) (1-Cys PRX) (24 kDa protein) (Acidic caicium-independent phospholipase P30041 PRDX6 A2) (aiPLA2) (EC 3.1 . 1 .-) (Antioxidant protein 224 FALSE FALSE FALSE FALSE FALSE FALSE 2) (Liver 2D page spot 4 ) (Non-selenium glutathione peroxidase) (NSGPx) (EC 1. 1 1.1.9) (Red blood ceils page spot 12)

Peroxisomal acyl-coenzyme A oxidase 1 ∞ Q15067 ACOX1 (AOX) (EC 1.3.3.6) (Palmitoyl-CoA oxidase) 660 FALSE FALSE FALSE FALSE FALSE FALSE (Straight-chain acyl-CoA oxidase) (SCOX)

Peroxisomal multifunctional enzyme type 2 (MFE-2) (17-beta-hydroxysferoid dehydrogenase 4) (17-beta-HSD 4) (D- bifunctional protein) (DBP) (Multifunctional protein 2) (MPF-2) (Short chain P51659 HSD17B4 dehydrogenase/reductase family 8C member 736 TRUE TRUE FALSE TRUE TRUE TRUE 1) [Cleaved into: (3R)-hydroxyacyl-CoA dehydrogenase (EC 1.1 . 1 .n12); Enoyl-CoA hydratase 2 (EC 4.2.1 .107) (EC 4.2.1 . 1 19) (3- alpha,7-alpha, 12-aipha-trihydroxy-5-beta- cholest-24-enoyl-CoA hydratase)] GRB10-interacting GYF protein 2 (PERQ - ,. .. „ - „ amino acid-rich with GYF domain-containing V 1299 FALSE FALSE FALSE FALSE TRUE FALSE protein 2) (Trinucleotide repeat-containsng gene 15 protein) 000541 PES1 Pescadi!!o homolog 588 TRUE TRUE TRUE FALSE FALSE TRUE PEST proteolytic signal-containing nuclear Q8WW12 PCNP protein (PCNP) (PEST-containing nuclear 178 FALSE FALSE FALSE FALSE FALSE FALSE protein) PH-interacting protein (PHIP) (!RS-1 PH Q8WWQ0 ΡΗ Ρ domain-binding protein) (WD repeat- 1821 FALSE FALSE FALSE FALSE FALSE FALSE containing protein 11) PHD finger protein 6 (PHD-like zinc finger Q8IWS0 PHF6 365 TRUE FALSE FALSE FALSE FALSE FALSE protein) PHD finger-like domain-containing protein 5A (PHD finger-like domain protein 5A) (Splicing Q7RTV0 PHF5A 110 FALSE FALSE FALSE FALSE FALSE FALSE factor SB-associated 14 kDa protein) (SF3b14b) Phenylalanine-tRNA iigase alpha subunit (EC Q9Y285 PARSA 6.1 . 1 .20) (CML33) (Phenylalanyi-tRNA 508 FALSE TRUE FALSE FALSE FALSE TRUE synthetase alpha subunit) (PheRS) Phenylalanine-tRNA iigase beta subunit (EC Q9NSD9 FARSB 6.1 . 1 .20) (Phenylalanyi-tRNA synthetase beta 589 TRUE TRUE TRUE FALSE FALSE FALSE subunit) (PheRS) Phosphate carrier protein, mitochondrial Q00325 SLC25A3 (Phosphate transport protein) (PTP) (Solute 362 FALSE FALSE FALSE FALSE FALSE FALSE carrier family 25 member 3) Phosphatidate cytidyiyitransferase 2 (EC 2.7.7.41) (CDP-DAG synthase 2) (CDP-DG synthase 2) (CDP-diacylglycerol synthase 2) 095674 CDS2 5 TRUE FALSE FALSE FALSE FALSE FALSE (CDS 2) (CDP-diglyceride pyrophosphatase 2) (CDP-diglyceride synthase 2) (CTP: phosphatidate cytidyiyitransferase 2)

Phosphatidylethanoiamine-binding protein 1 (PEBP-1) (HCNPpp) (Neuropolypeptide h3) (Prostatic-binding protein) (Raf kinase inhibitor 187 FALSE FALSE FALSE FALSE FALSE FALSE protein) (RKIP) [Cleaved into: Hippocampal cholinergic neurostimuiating peptide (HCNP)] Phosphatidylinositide phosphatase SAC1 (EC Q9NTJ5 SAC? 1 L 3.1 .3 -) (Suppressor of actin mutations - ike 587 FALSE FALSE FALSE FALSE FALSE FALSE protein) Phosphatidylinositol glycan anchor biosynthesis class U protein (Cell division Q9H490 P!GU 435 FALSE FALSE FALSE FALSE FALSE FALSE cycle protein 91-iike 1) (Protein CDC91-like 1) (GP transamidase component PIG-U) Phosphatidylinositol transfer protein beta P48739 PITPNB isoform (PI-TP-beta) (Ptdlns transfer protein 271 FALSE FALSE FALSE TRUE TRUE FALSE beta) (PtdlnsTP beta) Phosphatidylinositol-binding clathrin assembly Q13492 PICA L protein (Clathrin assembly lymphoid myeloid 652 FALSE FALSE TRUE FALSE FALSE FALSE leukemia protein) Phosphatidylserine synthase 1 (PSS-1) P48651 PTDSS1 (PtdSer synthase 1) (EC 2.7.8.29) (Serine- 473 FALSE FALSE FALSE TRUE TRUE FALSE exchange enzyme ) Phosphatidylserine synthase 2 (PSS-2) Q9BVG9 PTDSS2 (PtdSer synthase 2) (EC 2.7 8.29) (Serine- 487 FALSE FALSE FALSE FALSE TRUE TRUE exchange enzyme ) Phosphoglucomutase-2 (PGM 2) (EC 5.4 2.2) (Glucose phosphomutase 2) Q96GQ3 PGM2 612 FALSE FALSE FALSE FALSE FALSE FALSE (Phosphodeoxyribomutase) (Phosphopentomutase) (EC 5.4.2.7) Phosphoglycerate kinase 1 (EC 2.7.2.3) (Cell P00558 PGK1 migration-inducing gene 10 protein) (Primer 417 FALSE FALSE FALSE FALSE FALSE FALSE recognition protein 2) (PRP 2) Phosphoglycerate mutase 1 (EC 5.4.2.1 1) (EC 5.4.2.4) (BPG-dependent PGAM 1) P18669 PGA 1 254 FALSE FALSE FALSE FALSE FALSE FALSE (Phosphoglycerate mutase isozyme B) (PGAM- B) Phosphoiipase A-2-activating protein (PLA2P) Q9Y263 PLAA 795 FALSE FALSE FALSE FALSE FALSE FALSE (PLAP) Phosphoribosyl pyrophosphate synthase- associated protein 1 (PRPP synthase- Q14558 PRPSAP1 associated protein 1) (39 Da 356 FALSE FALSE FALSE FALSE FALSE FALSE phosphoribosypyrophosphate synthase- associated protein) (PAP39) Phosphoribosyl pyrophosphate synthase- associated protein 2 (PRPP synthase- 060256 PRPSAP2 associated protein 2) (41 kDa 369 FALSE FALSE FALSE FALSE TRUE TRUE phosphoribosypyrophosphate synthetase- associated protein) (PAP41)

Phosphoribosylformylgiycinamidine synthase (FGA synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide 015067 PFAS 1338 FALSE FALSE FALSE FALSE FALSE FALSE amidotransferase) (FGAR amidotransferase) (FGAR-AT) (Formylglycinamide ribotide amidotransferase)

Phosphoserine aminotransferase (EC oe Q9Y617 PSAT1 2.6.1 .52) (Phosphohydroxythreonine 370 FALSE FALSE FALSE TRUE TRUE FALSE aminotransferase) (PSAT) Pinin (140 kDa nuclear and cell adhesion- related phosphoprotein) (Desmosome- associated protein) (Domain-rich serine Q9H307 PNN 717 FALSE FALSE FALSE FALSE TRUE TRUE protein) (DRS protein) (DRSP) (Melanoma metastasis clone A protein) (Nuclear protein SDKS) (SR ike protein) Plasminogen activator inhibitor 1 RNA-binding Q8NC51 SERBP1 protein (PAH RNA-binding protein 1) (PA - 408 FALSE FALSE FALSE FALSE FALSE FALSE RBP1) (SERPINE1 mRNA-binding protein 1)

Q14651 PLS1 Plastin-1 (Intestine-specific piastin) (i-piastin) 629 TRUE FALSE FALSE FALSE FALSE FALSE Plastin-2 (L-plastin) (LC64P) (Lymphocyte P13796 LCP1 627 FALSE FALSE FALSE FALSE FALSE FALSE cytosolic protein 1) (LCP-1) Platelet-activating factor acetylhydrolase IB subunit alpha (Lissencephaiy-1 protein) (LIS- PAFAH1B P43034 1) (PAF acetylhydrolase 45 kDa subunit) (PAF- 410 FALSE FALSE FALSE FALSE FALSE FALSE 1 AH 45 kDa subunit) (PAF-AH alpha) (PAFAH alpha) Platelet-activating factor acetylhydrolase IB subunit beta (EC 3 . .1.47) (PAF PAFAH1B acetylhydrolase 30 kDa subunit) (PAF-AH 30 229 FALSE TRUE TRUE FALSE FALSE TRUE 2 kDa subunit) (PAF-AH subunit beta) (PAFAH subunit beta) Platelet-activating factor acetylhydrolase IB subunit gamma (EC 3.1 . 1 .47) (PAF PAFAH1B Q15102 acetylhydrolase 29 kDa subunit) (PAF-AH 29 231 TRUE TRUE FALSE TRUE FALSE FALSE 3 kDa subunit) (PAF-AH subunit gamma) (PAFAH subunit gamma) Poly [ADP-ribose] polymerase 1 (PARP-1) (EC 2.4.2.30) (ADP-ribosyltransferase PARP1 diphtheria toxin-like 1) (ARTD1) (NAD(+) ADP- 1014 FALSE FALSE FALSE FALSE FALSE FALSE oe -4 ribosyltransferase 1) (ADPRT 1) (Poly[ADP- ribose] synthase 1) Poly(A)-specific ribonuclease PARN (EC 3.1 .13.4) (Deadenyiating nuclease) 095453 PARN 639 FALSE FALSE FALSE FALSE FALSE FALSE (Deadenylation nuclease) (Polyadenylate- specific ribonuclease) Poly(rC)-binding protein 1 (Alpha-CP1) (Heterogeneous nuclear ribonucieoprotein E1) Q15365 PCBP1 356 FALSE FALSE FALSE FALSE FALSE FALSE (hnRNP E1) (Nucleic acid-binding protein SUB2.3) Poly(rC)-binding protein 2 (Alpha-CP2) Q15366 PCBP2 (Heterogeneous nuclear ribonucieoprotein E2) 365 FALSE FALSE FALSE FALSE FALSE FALSE (hnRNP E2) Poly(U)-binding-splicing factor PUF60 (60 kDa poly(U)-binding-splicing factor) (FUSE-binding Q9UHX1 PUF60 protein-interacting repressor) (FBP-interacting 559 FALSE FALSE FALSE FALSE FALSE FALSE repressor) (Ro-binding protein 1) (RoBP1) (Siah-binding protein 1) (Siah-BP1) Polyadenylate-binding protein 1 (PABP-1) P 1 1940 PABPC1 636 FALSE FALSE FALSE FALSE FALSE FALSE (Poly(A)-binding protein 1) Polyadenylate-binding protein 2 (PABP-2) (Poly(A)-binding protein 2) (Nuclear poly(A)- PABPN1 binding protein 1) (Poiy(A)-binding protein ) 306 TRUE TRUE FALSE FALSE FALSE FALSE (ΡΑΒ ) (Polyadenylate-binding nuclear protein 1) Polyadenylate-binding protein 4 (PABP-4) (Poly(A)-binding protein 4) (Activated-platelet Q13310 PABPC4 644 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) (APP-1) (Inducible poly(A)-binding protein) (iPABP) Polycomb protein EED (hEED) (Embryonic ectoderm development protein) (WD protein 075530 EED TRUE FALSE FALSE FALSE FALSE TRUE associating with integrin cytoplasmic tails 1) (WAIT-1) Polymerase delta-interacting protein 3 (46 kDa Q9BY77 POLDIP3 DNA polymerase delta interaction protein) 421 TRUE FALSE FALSE FALSE FALSE FALSE (p46) (S6K1 Aly/REF-like target) (SKAR) Polynucleotide 5'-hydroxyl-kinase NOL9 (EC Q5SY16 NOL9 702 FALSE FALSE FALSE FALSE FALSE FALSE 2 7.1.-) (Nucleolar protein 9) Polypyrimidine tract-binding protein 1 (PTB) (57 kDa RNA-binding protein PPTB-1) P26599 PTBP1 531 FALSE FALSE FALSE FALSE FALSE FALSE (Heterogeneous nuclear ribonucleoprotein I) (hnRNP ) Polyribonucleotide nucleotidyltransferase 1, mitochondrial (EC 2 7.7.8) (3'-5' RNA Q8TCS8 PNPT1 exonuclease OLD35) (PNPase old-35) 783 TRUE FALSE FALSE FALSE FALSE FALSE (Polynucleotide phosphorylase 1) (PNPase 1) (Polynucleotide phosphory!ase-!ike protein)

PRA1 family protein 3 (ADP-ribosylation factor like protein 6-interacting protein 5) (ARL-6- interacting protein 5) (Aip-5) (Cytoskeleton- reiated vitamin A-responsive protein) (Dermal 075915 ARL6IP5 papilla-derived protein 1 ) (GTRAP3-1 8) 188 FALSE FALSE FALSE FALSE FALSE FALSE (Glutamate transporter EAAC1 -interacting protein) ( 5) (Prenylated Rab acceptor protein 2) (Protein JWa) (Putative APK- activating protein P 27)

Pre-mRNA 3'-end-processing factor FIP1 Q6UN15 FIP1 L 1 (hFipl) (Fi P1-hke 1 protein) (Factor interacting 594 FALSE FALSE FALSE FALSE FALSE FALSE with PAP) (Rearranged in hypereosinophilia)

Pre-mRNA-processing factor 9 (EC 2.3.2.27) (Nuclear matrix protein 200) (PRP19/PS04 Q9UIV1S4 PRPF19 homolog) (hPso4) (RING-type E3 ubiquitin 504 FALSE FALSE FALSE FALSE FALSE FALSE transferase PRP19) (Senescence evasion factor) Pre-mRNA-processing factor 40 homolog A (Fas ligand-associafed factor 1) (Formin- binding protein 11) (Formin-binding protein 3) 075400 PRPF40A (Huntingtin yeast partner A) (Huntingtin- 957 FALSE FALSE FALSE TRUE TRUE TRUE interacting protein 10) (HIP-10) (Huntingtin- interacting protein A) (Renal carcinoma antigen NY-REN-6) Pre-mRNA-processing factor 6 (Androgen receptor N-terminal domain-transactivaiing 094906 PRPF6 protein 1) (ANT-1) (PRP6 homolog) (U5 TRUE TRUE FALSE FALSE FALSE FALSE snRNP-associated 102 kDa protein) (U5-102 kDa protein) Pre-mRNA-processing-splicing factor 8 (220 Q6P2Q9 PRPF8 kDa U5 snRNP-specific protein) (PRP8 FALSE FALSE FALSE FALSE FALSE FALSE homolog) (Splicing factor Prp8) (p220)

Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 312 FALSE FALSE FALSE FALSE FALSE FALSE Pre-mRNA-splicing factor ATP-dependent RNA heiicase DHX15 (EC 3.6.4.13) (ATP- 043143 DHX15 795 FALSE FALSE FALSE FALSE FALSE FALSE dependent RNA heiicase #46) (DEAH box protein 15) Pre-mRNA-splicing factor CWC22 homolog Q9HCG8 CWC22 9 8 TRUE FALSE FALSE FALSE TRUE FALSE (Nucampbolin homolog) (fSAPb) Pre-mRNA-splicing factor RB 22 (RNA- Q9NW64 binding motif protein 22) (Zinc finger CCCH 420 FALSE FALSE FALSE FALSE FALSE FALSE domain-containing protein 16) Pre-mRNA-splicing factor SPF27 (Breast carcinoma-amplified sequence 2) (DNA 075934 225 TRUE FALSE FALSE FALSE FALSE FALSE amplified in mammary carcinoma 1 protein) (Spliceosome-associated protein SPF 27)

Pre-mRNA-splicing factor SYF1 (Protein Q9HCS7 XAB2 855 FALSE TRUE FALSE TRUE TRUE TRUE HCNP) (XPA-binding protein 2) Pre-mRNA-splicing regulator WTAP (Female- iethal(2)D homolog) (hFL(2)D) (WT1- Q15007 WTAP 396 FALSE FALSE FALSE TRUE FALSE FALSE associafed protein) (Wilms tumor 1- associating protein) pre-rRNA processing protein FTSJ3 (EC 2.1 . 1 .-) (2 -O-ribose RNA meihyltransferase Q8IY81 FTSJ3 847 FALSE TRUE FALSE TRUE TRUE TRUE SPB1 homolog) (Protein ftsJ homolog 3) (Putative rRNA meihyltransferase 3) Q2NL82 TSR1 Pre-rRNA-processing protein TSR1 homolog 804 FALSE FALSE FALSE FALSE FALSE FALSE Q9UHV9 PFDN2 Prefoidin subunit 2 154 FALSE FALSE FALSE TRUE FALSE FALSE Prefoidin subunit 3 (HIBBJ46) (Von Hippel- P61758 VBP1 Lindau-binding protein 1) (VBP-1) (VHL- 197 FALSE FALSE FALSE FALSE FALSE FALSE binding protein 1) Prefoidin subunit 5 (C-Myc-binding protein Mm- Q99471 PFDN5 154 FALSE FALSE FALSE FALSE FALSE FALSE 1) ( yc modulator 1)

Presenilins-associated rhomboid-like protein, mitochondrial (EC 3.4.21 .105) (Mitochondrial Q9H300 PARL 379 FALSE FALSE FALSE FALSE FALSE FALSE intramembrane cleaving protease PARL) [Cleaved into: P-beta (Pbeta)]

Probable 28S rRNA (cytosine(4447)-C(5))- methyltransferase (EC 2.1 . 1 .-) (Nucleolar protein 1) (Nucleolar protein 2 homolog) P46087 NOP2 812 FALSE FALSE! FALSE FALSE F LS (Proliferating-cell nucleolar antigen p120) (Proliferation-associated nucleolar protein p120)

Probable ATP-dependent RNA helicase DDX17 (EC 3.6.4.13) (DEAD box protein 17) Q92841 DDX17 729 FALSE FALSE FALSE FALSE FALSE FALSE (DEAD box protein p72) (DEAD box protein p82) (RNA-dependent helicase p72)

Probable ATP-dependent RNA helicase DDX20 (EC 3 6.4.13) (Component of gems 3) Q9UHI6 DDX20 824 FALSE FALSE FALSE FALSE FALSE FALSE (DEAD box protein 20) (DEAD box protein DP 103) (Gemin-3) Probable ATP-dependent RNA helicase DDX23 (EC 3.6.4.13) (100 kDa U5 snRNP- Q9BUQ8 DDX23 820 FALSE FALSE FALSE TRUE FALSE specific protein) (DEAD box protein 23) (PRP28 homolog) (U5-100kD)

Probable ATP-dependent RNA helicase Q96GQ7 DDX27 796 FALSE TRUE FALSE FALSE FALSE FALSE DDX27 (EC 3.6.4.13) (DEAD box protein 27) Probable ATP-dependent RNA helicase Q7L014 DDX46 DDX46 (EC 3.6 4.13) (DEAD box protein 46) 1031 TRUE TRUE FALSE TRUE FALSE FALSE (PRP5 homolog) Probable ATP-dependent RNA helicase Q9H0S4 DDX47 455 TRUE FALSE FALSE TRUE FALSE TRUE DDX47 (EC 3.6.4.13) (DEAD box protein 47) Probable ATP-dependent RNA helicase DDX5 P17844 DDX5 (EC 3.6.4.13) (DEAD box protein 5) (RNA 614 FALSE FALSE FALSE FALSE FALSE FALSE helicase p68) Probable ATP-dependent RNA helicase Q9Y2R4 DDX52 DDX52 (EC 3.6.4.13) (ATP-dependent RNA 599 TRUE TRUE FALSE FALSE FALSE FALSE helicase ROK1-like) (DEAD box protein 52)

Probable ATP-dependent RNA helicase DDX56 (EC 3.6.4.13) (ATP-dependent 6 1 kDa Q9NY93 DDX56 547 FALSE FALSE FALSE FALSE FALSE FALSE nucleolar RNA helicase) (DEAD box protein 21) (DEAD box protein 56)

Probable ATP-dependent RNA helicase DDX6 P26196 DDX6 (EC 3.6.4.13) (ATP-dependent RNA helicase 483 FALSE FALSE FALSE FALSE FALSE FALSE p54) (DEAD box protein 6) (Oncogene RCK) Probable cytosolic iron-sulfur protein assembly 076071 CIA01 protein CIA01 (WD repeat-containing protein 339 TRUE FALSE FALSE TRUE FALSE TRUE 39)

Probable dimethyladenosine transferase (EC 2.1 . 1 .183) (DIM1 dimethyladenosine transferase 1 homolog) (DI 1 dimethyladenosine transferase 1-like) Q9UNQ2 DIMT1 (Probable 18S rRNA (adenine! 1779)- 313 TRUE FALSE FALSE FALSE FALSE FALSE N(6)/adenine(1 780)-N(6))- dimethy!transferase) (Probable 18S rRNA dimethylase) (Probable S-adenosylmethionine- 6-N',N'-adenosyl(rRNA) dimethyitransferase) Probable leucine-tRNA ligase, mitochondrial Q15031 LARS2 (EC 6 . .1.4) (Leucyi-tRNA synthetase) 903 FALSE FALSE FALSE FALSE FALSE FALSE (LeuRS) BNA1 BP ° rRNA-processing protein EBP2 Q99848 _ (EBNA1 -binding protein 2) (Nucleolar protein 306 FALSE FALSE FALSE TRUE TRUE TRUE p40)

Probable tRNA N8~adenosine threonylcarbamoyltransferase (EC 2.3 1.234) (N6-L-threonylcarbamoyladenine synthase) (t(6)A synthase) (O-sialoglycoprotein

Q9NPF4 OSGEP endopeptidase) (hOSGEP) (t(6)A37 33 F L3 Ε A Ξ F L F Ε FA Ξ FA L EE threonylcarbamoyladenosine biosynthesis protein OSGEP) (tRNA threonylcarbamoyladenosine biosynthesis protein OSGEP)

Probable ubiquitin carboxyl-terminal hydrolase FAF-X (EC 3.4.19.12) (Deubiquitinating enzyme FAF-X) (Fat facets in mammals) USP9X (hFA ) (Fat facets protein-related, X-linked) 2570 FALSE FALSE FALSE TRUE FALSE FALSE (Ubiquitin thioesterase FAF-X) (Ubiquitin- specific protease 9 , chromosome) (Ubiquitin- specific-processing protease FAF-X)

Profilin-1 (Epididymis tissue protein Li 184a) P07737 PFN1 140 FALSE FALSE FALSE FALSE FALSE FALSE (Profilin ) Programmed cell death 6-interacting protein (PDCD6-interacting protein) (ALG-2- Q8WUM4 PDCD6IP 868 FALSE FALSE FALSE FALSE FALSE FALSE interacting protein 1) (ALG-2-interacting protein X) (Hp95)

Programmed cell death protein 4 (Neoplastic PDCD4 transformation inhibitor protein) (Nuclear 469 FALSE FALSE FALSE FALSE FALSE FALSE antigen H731-like) (Protein 197/1 5a) Programmed eel! death protein 5 (TF-1 cell 014737 PDCD5 apoptosis-related protein 19) (Protein 125 FALSE FALSE FALSE FALSE FALSE FALSE TFAR19) Programmed cell death protein 6 (Apoptosis- 075340 PDCD6 191 TRUE TRUE FALSE FALSE FALSE FALSE linked gene 2 protein homolog) (ALG-2)

P35232 PHB Prohibitin 272 FALSE FALSE FALSE FALSE FALSE FALSE Prohibiiin-2 (B-celi receptor-associated protein Q99623 PHB2 BAP37) (D-prohibitin) (Repressor of estrogen 299 FALSE FALSE FALSE FALSE FALSE FALSE receptor activity) Prolactin regulatory element-binding protein Q9HCU5 PREB (Mammalian guanine nucleotide exchange 417 FALSE FALSE FALSE FALSE TRUE TRUE factor mSec12) Proliferating ce l nuclear antigen (PCNA) P12004 PCNA 261 FALSE FALSE FALSE FALSE FA LSE F (Cyclin) Proliferation-associated protein 2G4 (Cell Q9UQ80 PA2G4 cycle protein p38-2G4 homolog) (hG4-1) 394 FALSE FALSE FALSE TRUE FALSE FALSE (ErbB3-binding protein 1) 4- Proline-, glutamic acid- and leucine-rich protein 1 (Modulator of non-genomic activity of Q8IZL8 PELP1 1130 FALSE FALSE FALSE TRUE FALSE FALSE estrogen receptor) (Transcription factor HMX3) Prolyl endopeptidase (PE) (EC 3.4.2 1 26) P48147 PREP 710 FALSE FALSE FALSE FALSE FALSE FALSE (Post-proline cleaving enzyme) Propionyl-CoA carboxylase alpha chain, mitochondrial (PCCase subunit alpha) (EC P05165 PCCA 728 FALSE FALSE FALSE FALSE FALSE FALSE 6.4.1 .3) (Propanoyl-CoA:carbon dioxide ligase subunit alpha) Propionyl-CoA carboxylase beta chain, mitochondrial (PCCase subunit beta) (EC P05166 PCCB 539 FALSE FALSE FALSE FALSE FALSE FALSE 6.4.1 .3) (Propanoyl-CoA: carbon dioxide ligase subunit beta) Prostaglandin E synthase 3 (EC 5.3 99.3) (Cytosolic prostaglandin E2 synthase) Q15185 PTGES3 (cPGES) (Hsp90 co-chaperone) 160 FALSE FALSE FALSE TRUE TRUE TRUE (Progesterone receptor complex p23) (Telomerase-binding protein p23)

Proteasomal ubiquitin receptor ADRM1 ( 1 10 kDa cell membrane glycoprotein) (Gp1 10) Q16186 ADR 1 (Adhesion-regulating moiecLfle 1) (ARM-1) FALSE FALSE FALSE TRUE TRUE TRUE (Proteasome regulatory particle non-ATPase 13) (hRpn13) (Rpn13 ho o og)

Proteasome activator complex subunit 2 ( 1 1S regulator complex subunit beta) (REG-beta) Q9UL46 PS E2 (Activator of multicatalytic protease subunit 2) 239 FALSE FALSE FALSE FALSE TRUE TRUE (Proteasome activator 28 subunit beta) (PA28b) (PA28beta) Proteasome activator complex subunit 3 ( 1 1S regulator complex subunit gamma) (REG- •J\ gamma) (Activator of multicatalytic protease P61289 PS E3 254 FALSE FALSE FALSE TRUE FALSE TRUE subunit 3) (Ki nuclear autoanfigen) (Proteasome activator 28 subunit gamma) (PA28g) (PA28gamma) Proteasome assembly chaperone 1 (PAC-1) (Chromosome 2 1 leucine-rich protein) (C21- 095456 PSMG1 288 FALSE FALSE FALSE FALSE FALSE FALSE LRP) (Down syndrome critical region protein 2) Q92530 PSMF1 Proteasome inhibitor PI31 subunit (hPI31) 271 FALSE TRUE TRUE FALSE FALSE FALSE Proteasome subunit alpha type-1 (EC 3.4.25.1) (30 kDa prosomal protein) (PROS- 30) (Macropain subunit C2) (Multicatalytic P25786 PS A 1 263 FALSE FALSE FALSE FALSE FALSE FALSE endopeptidase complex subunit C2) (Proteasome component C2) (Proteasome nu chain) Proteasome subunit alpha type-2 (EC 3.4.25 1) (Macropain subunit C3) P25787 PSMA2 234 FALSE FALSE FALSE TRUE TRUE TRUE (Multicatalytic endopeptidase complex subunit C3) (Proteasome component C3) Proteasome subunit alpha type-3 (EC 3.4.25.1) (Macropain subunit C8) P25788 PS A3 255 FALSE FALSE FALSE FALSE FALSE FALSE (Multicatalytic endopeptidase complex subunit C8) (Proteasome component C8) Proteasome subunit alpha type-4 (EC 3.4.25.1) (Macropain subunit C9) P25789 PSMA4 (Multicatalytic endopeptidase complex subunit 261 FALSE FALSE FALSE FALSE TRUE TRUE C9) (Proteasome component C9) (Proteasome subunit L) Proteasome subunit alpha type-5 (EC 3.4.25.1) (Macropain zeta chain) P28066 PSMA5 241 TRUE TRUE FALSE FALSE FALSE FALSE (Multicatalytic endopeptidase complex zeta chain) (Proteasome zeta chain) Proteasome subunit alpha type-6 (EC 3.4.25.1) (27 kDa prosomal protein) (PROS- P609Q0 PSMA6 27) (p27K) (Macropain iota chain) 246 FALSE FALSE FALSE FALSE FALSE FALSE (Multicatalytic endopeptidase complex iota chain) (Proteasome iota chain) Proteasome subunit alpha type-7 (EC 014818 PSMA7 3.4.25.1) (Proteasome subunit RC6-1) 248 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome subunit XAPC7) Proteasome subunit beta type-1 (EC 3.4.25.1) (Macropain subunit CS) (Multicatalytic P20618 PSMB1 endopeptidase complex subunit C5) 241 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome component C5) (Proteasome gamma chain) Proteasome subunit beta type-2 (EC 3.4.25.1) (Macropain subunit C7-I) (Multicatalytic P49721 PSMB endopeptidase complex subunit C7-I) (Proteasome component C7~i) Proteasome subunit beta type-3 (EC 3 4.25.1) P49720 PSMB3 (Proteasome chain 13) (Proteasome 05 FALSE FALSE FALSE TRUE FALSE FALSE component C10-II) (Proteasome theta chain)

Proteasome subunit beta type~4 (EC 3.4.25.1) (26 kDa prosoma! protein) (HsBPROS26) (PROS-26) (Macropain beta chain) P28070 PS B4 264 FALSE FALSE FALSE FALSE FALSE FALSE (Multicatalytic endopeptidase complex beta chain) (Proteasome beta chain) (Proteasome chain 3) (HsN3) Proteasome subunit beta type-5 (EC 3.4.25.1) (Macropain epsiion chain) (Multicatalytic endopeptidase complex epsiion chain) P28074 PSMB5 263 FALSE FALSE FALSE TRUE TRUE TRUE (Proteasome chain 6) (Proteasome epsiion chain) (Proteasome subunit MB1) (Proteasome subunit X) Proteasome subunit beta type-6 (EC 3.4.25.1) (Macropain delta chain) (Multicatalytic P28072 PSIVIB6 endopeptidase complex delta chain) 239 FALSE FALSE FALSE FALSE FALSE FALSE (Proteasome delta chain) (Proteasome subunit Y) Proteasome subunit beta type-7 (EC 3.4.25.1) (Macropain chain Z) (Multicatalytic PSMB7 277 FALSE FALSE FALSE FALSE FALSE FALSE endopeptidase complex chain Z) (Proteasome subunit Z)

P 1 1171 EPB41 Protein 4.1 (P4.1) (4.1 R) (Band 4.1) (EPB4.1) 864 FALSE FALSE FALSE FALSE FALSE FALSE

Protein ABHD16A (EC 3.-.- -) (Alpha/beta hydrolase domain-containing protein 16A) 095870 ABHD16A 558 FALSE FALSE FALSE TRUE FALSE FALSE (Abhydrolase domain-containing protein 16A) (HLA-B-associated transcript 5) (Protein G5)

Protein arginine N-methyltransferase 1 (EC 2.1 . 1 .319) (Histone-arginine N- PRMT1 361 FALSE FALSE FALSE FALSE FALSE FALSE methyltransferase PRMT1) (Interferon receptor 1-bound protein 4) Protein arginine N-methyltransferase 5 (EC 2.1 .1 .320) (72 kDa ICln-binding protein) (Histone-arginine N-methyltransferase 014744 PR T5 PR T5) (Jak-binding protein 1) (Shk1 kinase- 637 TRUE TRUE FALSE FALSE FALSE FALSE binding protein 1 homolog) (SKB1 homolog) (SKBI Hs) [Cleaved into: Protein arginine N- methyltransferase 5 , N termina y processed]

Q9H2C2 ARV1 Protein ARV1 (hARV1) 271 FALSE FALSE FALSE FALSE FALSE FALSE Protein BUD31 homolog (Protein EDG-2) P41223 BUD31 144 FALSE FALSE FALSE TRUE FALSE FALSE (Protein G10 homolog) Protein CIP2A (Cancerous inhibitor of PP2A) Q8TCG1 KSAA1524 905 FALSE FALSE FALSE FALSE FALSE FALSE (p90 autoantigen) Q5TDH0 Protein DD homolog 2 399 FALSE FALSE FALSE FALSE FALSE TRUE

Protein DJ-1 (DJ-1) (Oncogene DJ1) (Parkinson disease protein 7) (Parkinsonism- Q99497 PARK7 189 FALSE FALSE FALSE FALSE FALSE FALSE associated deglycase) (Protein deglycase DJ- 1) (EC 3.1 .2.-) (EC 3.5.1 .124) P35659 DEK Protein DEK 375 TRUE TRUE TRUE TRUE TRUE TRUE Protein diaphanous homolog 1 (Diaphanous- 060610 DIAPH1 1272 FALSE FALSE FALSE FALSE FALSE FALSE related formin-1) (DRF1) Protein diaphanous homolog 3 (Diaphanous- Q9NSV4 DIAPH3 1193 FALSE FALSE FALSE FALSE FALSE FALSE related formin-3) (DRF3) ( Dia2)

Protein disulfide-isomerase A3 (EC 5.3.4.1) (58 kDa glucose-regulated protein) (58 kDa microsomal protein) (p58) (Disulfide P30101 PDIA3 isomerase ER-60) (Endoplasmic reticulum 505 FALSE FALSE FALSE FALSE FALSE FALSE resident protein 57) (ER protein 57) (ERp57) (Endoplasmic reticulum resident protein 60) (ER protein 60) (ERp60) Protein disulfide-isomerase A4 (EC 5.3.4.1) (Endoplasmic reticulum resident protein 70) P13667 PD1A4 (ER protein 70) (ERp70) (Endoplasmic 645 TRUE FALSE FALSE FALSE FALSE FALSE reticulum resident protein 72) (ER protein 72) (ERp-72) (ERp72) Protein disulfide-isomerase A5 (EC 5.3.4.1) Q14554 PDIA5 519 FALSE FALSE FALSE FALSE TRUE FALSE (Protein disulfide isomerase-related protein)

Protein disulfide-isomerase A6 (EC 5.3.4.1) (Endoplasmic reticulum protein 5) (ER protein Q15084 PDIA6 FALSE FALSE FALSE FALSE FALSE FALSE 5) (ERp5) (Protein disulfide isomerase P5) (Thioredoxin domain-containing protein 7)

Protein disulfide-isomerase (PDI) (EC 5.3.4.1) P07237 P4HB (Cellular thyroid hormone-binding protein) 508 FALSE FALSE FALSE FALSE FALSE FALSE (Prolyl 4-hydroxylase subunit beta) (p55) Protein disulfide-isomerase T X3 (EC 5.3.4.1) (Thioredoxin domain-containing Q96JJ7 T X3 454 FALSE FALSE FALSE FALSE TRUE TRUE protein 10) (Thioredoxin-re!ated transmembrane protein 3) Protein ERGiC-53 (ER-Goigi intermediate compartment 53 kDa protein) (Gp58) P49257 L A N1 510 TRUE TRUE FALSE TRUE TRUE TRUE (Intracellular mannose-specific lectin MR60) (Lectin mannose-binding 1) FA 14A Q9NRY5 Protein FA 114A2 505 FALSE FALSE FALSE FALSE FALSE FALSE 2 RETREG Q86VR2 Reticulophagy regulator 3 466 FALSE FALSE FALSE FALSE FALSE FALSE 3 Protein FAM162A (E2-induced gene 5 protein) Q96A26 FAM162A (Growth and transformation-dependent 154 FALSE FALSE FALSE TRUE TRUE TRUE protein) (HGTD-P) Q9NUQ9 FAM49B Protein FA 49B (L1) 324 FALSE FALSE FALSE FALSE FALSE FALSE Q8NCA5 FAM98A Protein FA 98A 519 TRUE FALSE FALSE FALSE FALSE FALSE Q52LJ0 FAM98B Protein FA 98B 330 FALSE FALSE FALSE FALSE FALSE FALSE Protein farnesyltransferase/geranyigeranyltransferase type-1 subunit alpha (EC 2.5.1 58) (EC 2.5.1 .59) (CAAX farnesyltransferase subunit Ρ49354 FNTA 379 FALSE FALSE FALSE TRUE TRUE FALSE alpha) (FTase-a!pha) (Ras proteins prenyitransferase subunit alpha) (Type protein geranyl-geranyltransferase subunit alpha) (GGTase-l-alpha) Q 13045 FLU Protein flightless- 1 homolog 1269 FALSE FALSE TRUE FALSE FALSE FALSE

Q14331 FRG1 Protein FRG1 (FSHD region gene 1 protein) 258 TRUE TRUE FALSE TRUE TRUE TRUE

Q9BTY7 HGH1 Protein HGH1 homolog 390 FALSE TRUE TRUE FALSE FALSE FALSE Q8N5 9 JAG 1 Protein jagunal homolog 1 183 FALSE TRUE FALSE TRUE TRUE FALSE Protein kinase C beta type (PKC-B) (PKC- Ρ05771 PRKCB 671 FALSE FALSE FALSE FALSE FALSE TRUE beta) (EC 2.7.1 1.13)

Protein kinase C iota type (EC 2.7.1 1.13) Ρ41743 PRKCI (Atypical protein kinase C-lambda/iota) (PRKC- 596 F S ! F F L F LS FALSE FA LS ο ο iambda/iota) (aPKC-lambda/iota) (nPKC-iota) Protein kinase C-binding protein 1 (Cutaneous T-ce lymphoma-associated antigen se14-3) Q9ULU4 Z Y D8 (CTCL-associated antigen se1 4-3) (Rack7) 1186 FALSE FALSE FALSE FALSE TRUE FALSE (Zinc finger Y D domain-containing protein

T EIV 1 7 Protein kish-A (Transmembrane protein Q8TBQ9 72 FALSE FALSE F L FA L FALSE FALSE A (Transmembrane protein 167A) Erbin (Densin~180-like protein) (Erbb2- Q96RT1 ERBIN 1412 FALSE FALSE FALSE FALSE FALSE FALSE interacting protein) (Protein LAP2)

Protein LYRIC (3D3/LYRIC) (Astrocyte elevated gene-1 protein) (AEG-1) (Lysine-rich Q86UE4 1TDH 582 TRUE TRUE FALSE FALSE FALSE FALSE CEACAM1 co-isolated protein) (Metadherin) (Metastasis adhesion protein)

Q96A72 MAGOHB Protein mago nashi homolog 2 148 FALSE FALSE FALSE TRUE TRUE TRUE Protein ΑΚ 6 homolog (ΝΝΡ 78) (Protein j ybAYU A ib 300 TRUE FALSE TRUE TRUE FALSE FALSE K ) N!PSNAP Protein NipSnap homo!og 2 (NipSnap2) 075323 286 FALSE FALSE FALSE FALSE FALSE FALSE 2 (Gliobiastoma-amplified sequence)

Protein PAT1 homolog 1 (PAT1-!ike protein 1) Q86TB9 PATL1 770 FALSE FALSE FALSE FALSE FALSE FALSE (Protein PAT1 homolog b) (Patlb) (hPatlb)

PELO Protein pelota homolog (EC 3.1 .-.-) 385 FALSE FALSE FALSE FALSE FALSE FALSE

Protein phosphatase 1 regulatory subunit 12A PPP1 R12 (Myosin phosphatase-targeting subunit 1) O14974 330 FALSE FALSE FALSE FALSE TRUE TRUE A (Myosin phosphatase target subunit 1) (Protein phosphatase myosin-binding subunit)

Protein phosphatase 1B (EC 3.1 .3.16) 075688 PP 1B (Protein phosphatase 2C isoform beta) (PP2C- 479 FALSE FALSE FALSE FALSE FALSE FALSE beta) Protein phosphatase 1F (EC 3.1.3.16) (Ca(2+)/calmodulin-dependent protein kinase o P49593 PP 1F phosphatase) (CaM-kinase phosphatase) 454 FALSE FALSE FALSE FALSE FALSE FALSE (CaMKPase) (Partner of P X 2) (Protein fem-2 homolog) (hFem-2) Protein phosphatase 1G (EC 3.1 .3.16) (Protein phosphatase 1C) (Protein 015355 PPM1G phosphatase 2C isoform gamma) (PP2C- 546 FALSE FALSE FALSE FALSE FALSE FALSE gamma) (Protein phosphatase magnesium- dependent 1 gamma) Protein phosphatase methylesterase 1 (P E- Q9Y570 PP E1 386 FALSE FALSE FALSE FALSE FALSE FALSE 1) (EC 3 1.1.89) Protein PML (Promyelocytic leukemia protein) P29590 PML (RING finger protein 71) (Tripartite motif- 882 FALSE TRUE FALSE TRUE TRUE TRUE containing protein 19) Protein RCC2 (RCC1-iike protein TD-60) Q9P258 522 FALSE FALSE FALSE FALSE FALSE FALSE (Telophase disk protein of 60 kDa) 015258 RER1 Protein RER1 196 FALSE FALSE FALSE TRUE FALSE FALSE Protein RRP5 hornolog (NF-kappa-B-binding Q 14690 PDCD1 protein) (NFBP) (Programmed cell death 1871 TRUE TRUE TRU E TRUE FALSE FALSE protein 11) Q96ER3 SAAL1 Protein SAAL1 474 FALSE FALSE TRUE FALSE FALSE FALSE Protein SEC1 3 homolog (GATOR complex P55735 SEC1 3 protein SEC1 3) (SEC1 3-like protein 1) 322 TRUE TRUE TRUE FALSE FALSE FALSE (SEC1 3-reiated protein)

Protein SGT1 homolog (Protein 40-6-3) (Sgt1 ) Q9Y2Z0 SUGT1 365 TRUE TRUE FALSE TRUE TRUE TRUE (Suppressor of G2 allele of SKP1 homolog)

Protein SON (Bax antagonist selected in saccharomyces 1) (BASS1 ) (Negative P 18583 2426 FALSE FALSE FALSE FALSE FALSE FALSE regulatory element-binding protein) (NRE~ binding protein) (Protein DBP-5) (SONS) Q9Y2G9 SBN02 Protein strawberry notch homolog 2 1366 FALSE FALSE FALSE FALSE FALSE FALSE

Protein TBRG4 (Cell cycle progression restoration protein 2) (Cell cycle progression ο Q969Z0 TBRG4 protein 2) (FAST kinase domain-containing 631 FALSE TRUE FALSE FALSE FALSE TRUE protein 4) (Transforming growth factor beta regulator 4)

Protein transport protein Sec1 6A (SEC1 6 0 15027 SEC1 6A 2179 FALSE FALSE FALSE FALSE FALSE FALSE homolog A) Protein transport protein Sec23A (SEC23- Q15436 SEC23A 765 FALSE FALSE FALSE FALSE FALSE FALSE related protein A) Protein transport protein Sec23B (SEC23- Q 15437 SEC23B 767 FALSE FALSE FALSE TRU E TRUE TRUE related protein B) Protein transport protein Sec24B (SEC24- 095487 SEC24B 1268 FALSE FALSE FALSE FALSE FALSE FALSE related protein B) Protein transport protein Sec24C (SEC24- P53992 SEC24C 1 FALSE FALSE FALSE FALSE FALSE FALSE reiated protein C)

Protein transport protein Sec31 A (ABP1 25) 094979 SEC31 A (ABP1 30) (SEC31 -like protein 1) (SEC31 - 1220 FALSE FALSE FALSE FALSE FALSE TRUE related protein A) (Web1 -like protein) « Protein transport protein Sec61 subunit alpha > 476 TRUE FALSE TRUE FALSE FALSE FALSE !soform 1 (Sec61 alpha-1 )

P60468 SEC61 B Protein transport protein Sec61 subunit beta FALSE FALSE FALSE FALSE FALSE FALSE

Q70J99 UNCI 3D Protein unc-1 3 homolog D (Mun 3-4) FALSE FALSE FALSE FALSE FALSE FALSE Protein unc-45 homolog A (Unc-45A) (GCUNC- Q9H3U 1 UNC45A 45) (Smooth muscle cell-associated protein 1) FALSE TRUE TRUE FALSE FALSE TRUE (SMAP-1 ) Protein Y IF B (YI P 1-interacting factor Q5BJH7 Y IF1B 3 14 TRUE FALSE FALSE FALSE FALSE FALSE homolog B) Protein-glutamate O-methyltransferase (EC Q9H993 A R T1 441 FALSE FALSE FALSE FALSE FALSE FALSE 2 .1.1.-) (Acidic residue methyltransferase 1)

Protein-L-isoaspartate(D-aspartate) O- methyltransferase (PIMT) (EC 2 .1.1.77) (L- isoaspartyl protein carboxyi methyltransferase) P22061 PC T 1 227 FALSE FALSE FALSE FALSE FALSE TRUE (Protein L-isoaspartyl/D-aspartyl ο methyltransferase) (Protein-beta-aspartate methyltransferase)

Prothymosin alpha [Cleaved into: Prothymosin P06454 PT A alpha, N~terminaliy processed; Thymosin 111 FALSE FALSE FALSE FALSE FALSE FALSE alpha-1 ] Pumilio homolog 3 (HBV X-transactivated gene 5 protein) (HBV XAg-transactivated Q 15397 PU 3 648 TRUE FALSE FALSE FALSE FALSE FALSE protein 5) (Minor histocompatibility antigen HA- 8) (HLA-HAS) Purine nucleoside phosphorylase (PNP) (EC P00491 PNP 2 4.2.1) (Inosine phosphorylase) ( Inosine- 89 FALSE FALSE FALSE TRU E TRUE FALSE guanosine phosphorylase) Puromycin-sensitive aminopepfidase (PSA) P55786 NPEPPS (EC 3.4. 11.14) (Cytosol aianyl ) 1 9 TRUE FALSE FALSE TRUE TRUE FALSE aminopeptidase) (AAP-S) ATX 7L3 Q96GX2 Putative ataxin-7-iike protein 3B 97 FALSE FALSE FALSE FALSE FALSE FALSE Putative ATP-dependent RNA helicase Q7L2E3 DHX30 1194 TRUE TRUE TRUE FALSE TRUE TRUE DHX30 (EC 3.6.4.13) (DEAH box protein 30) Putative coiied-coil-helix-coiled-coil-helix CHCHD2 domain-containing protein CHCHD2P9, Q5T1J5 FALSE FALSE FALSE FALSE FALSE FAL P9 mitochondria! (Coiled-coil-helix-coiled-coil- helix domain-containing 2 pseudogene 9) Putative helicase OV-10 (EC 3.6.4.13) Q9HCE1 OV 10 (Armitage homoiog) (Moioney leukemia virus 33 FALSE FALSE FALSE FALSE FALSE FALSE 10 protein) Putative mitochondria! import inner membrane Q5SRD1 TIM 23B 257 FALSE TRUE TRUE FALSE FALSE FALSE trans!ocase subunit Tim23B

Putative oxidoreductase GLYR1 (EC 1.-.-.-) (3- hydroxyisobutyrate dehydrogenase-like Q49A26 GLYR1 protein) (Cytokine-like nuclear factor N-PAC) 553 TRUE FALSE FALSE FALSE FALSE FALSE (Giyoxylate reductase 1 homo!og) (Nuclear protein NP60) (Nuclear protein of 60 kDa) ο Putative pre-mRNA-splicing factor ATP- dependent RNA helicase DHX16 (EC 060231 DHX16 1041 FALSE FALSE FALSE FALSE FALSE FALSE 3.6.4.13) (ATP-dependent RNA helicase #3) (DEAH-box protein 16)

Putative RNA-binding protein 15 (One-twenty Q96T37 RB 15 977 FALSE FALSE FALSE FALSE FALSE FALSE two protein 1) (RNA-binding motif protein 15) Putative RNA-binding protein Luc7-!ike 1 Q9NQ29 LUC7L FALSE FALSE FALSE FALSE FALSE FALSE (Putative SR protein LUC7B1) (SR+89) Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 FALSE FALSE FALSE FALSE FALSE FALSE SNRPGP Putative small nuclear ribonucleoprotein G-like A8 D9 TRUE FALSE FALSE FALSE FALSE FALSE 15 protein 15 Putative transferase CAF17, mitochondrial Q5T440 IBA57 (EC 2.1 .-.-) (Iron-sulfur cluster assembly factor 356 TRUE FALSE FALSE FALSE FALSE FALSE homoiog) Pyrroline-5-carboxylate reductase 1, P32322 PYCR1 mitochondrial (P5C reductase 1) (P5CR 1) 319 TRUE TRUE FALSE FALSE FALSE TRUE (EC 1.5.1 .2) Pyrroiine-5-carboxyiate reductase 2 (P5C Q96C36 PYCR2 320 FALSE FALSE FALSE TRUE FALSE TRUE reductase 2) (P5CR 2) (EC 1.5 1.2) Pyruvate carboxylase, mitochondrial (EC P 1 1498 PC 1178 FALSE FALSE FALSE FALSE FALSE FALSE 6.4.1 .1) (Pyruvic carboxylase) (PCB)

Pyruvate dehydrogenase E 1 component P08559 PDHA1 subunit alpha, somatic form, mitochondrial 390 FALSE TRUE FALSE TRUE FALSE FALSE (EC 1.2.4.1) (PDHE1-A type I)

Pyruvate dehydrogenase E 1 component P 1 1177 PDHB subunit beta, mitochondrial (PDHE1-B) (EC 359 FALSE FALSE FALSE TRUE TRUE TRUE 1.2.4.1) Pyruvate kinase PKLR (EC 2.7.1 .40) (Pyruvate kinase 1) (Pyruvate kinase P30613 PKLR 574 FALSE FALSE! FALSE FALSE FALSE isozymes L R) (R-type/L-type pyruvate kinase) (Red cell/liver pyruvate kinase)

Pyruvate kinase PKM (EC 2.7.1 .40) (Cytosoiic thyroid hormone-binding protein) (CTHBP) ο (Opa-interacting protein 3) (OIP-3) (Pyruvate •J\ Ρ 14618 PKI 531 FALSE FALSE TRUE FALSE FALSE FALSE kinase 2/3) (Pyruvate kinase muscle isozyme) (Thyroid hormone-binding protein 1) (THBP1) (Tumor M2-PK) (p58)

Quinone oxidoreductase (EC 1.6.5.5) Q08257 CRYZ 329 TRUE FALSE FALSE TRUE FALSE TRUE (NADPH:quinone reductase) (Zeta-crystallin)

Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate P31 150 GDI1 447 FALSE FALSE FALSE FALSE FALSE FALSE dissociation inhibitor 1) (GDI-1) (Oiigophrenin- 2) (Protein XAP-4) Rab GDP dissociation inhibitor beta (Rab GDI P50395 GDI2 beta) (Guanosine diphosphate dissociation 445 FALSE FALSE FALSE FALSE FALSE FALSE inhibitor 2) (GD!-2)

Rab3 GTPase-activating protein catalytic RAB3GA Q 15042 subunit (RAB3 GTPase-activating protein 130 981 FALSE FALSE FALSE FALSE FALSE FALSE P 1 kDa subunit) (Rab3-GAP p130) (Rab3-GAP) Rab3 GTPase-activaiing protein non-catalytic subunit (RGAP-iso) (Rab3 GTPase-activating RAB3GA Q9H2M9 protein 150 kDa subunit) (Rab3-GAP p150) 1393 TRUE TRUE TRUE TRUE FALSE TRUE Ρ2 (Rab3-GAP150) (Rab3-GAP regulatory subunit)

RAC-beta serine/threonine-protein kinase (EC Ρ 31751 Α Τ2 2.7.1 1.1) (Protein kinase Akt-2) (Protein 481 FALSE FALSE FALSE FALSE FALSE FALSE kinase B beta) (P B beta) (RAC-PK-beta)

Ρ35241 RDX Raclixin 583 FALSE FALSE FALSE FALSE FALSE FALSE RANGAP Ρ46060 Ran GTPase-activating protein 1 (RanGAPI) 587 TRUE TRUE TRUE FALSE FALSE FALSE 1 Ran-binding protein 9 (RanBP9) (BPM-L) Q96S59 RANBP9 (BPM90) (Ran-binding protein M) (RanBPM) 729 FALSE FALSE FALSE FALSE TRUE FALSE (RanBP7) Ran-specific GTPase-activating protein (Ran- Ρ43487 RANBP1 2 1 FALSE FALSE FALSE FALSE FALSE FALSE binding protein 1) (RanBPI)

ο Rap1 GTPase-GDP dissociation stimulator 1 RAP1GD (Exchange factor smgGDS) (SMG GDS Ρ52306 6 7 FALSE FALSE FALSE TRUE TRUE FALSE S 1 protein) (S G P21 stimulatory GDP/GTP exchange protein)

Ras GTPase-activating protein-binding protein 1 (G3BP-1) (EC 3.6.4.12) (EC 3.6.4.13) (ATP- Q13283 G3BP1 466 FALSE FALSE FALSE TRUE FALSE FALSE dependent DNA helicase Vlll) (hDH Vlll) (GAP SH3 domain-binding protein 1) Ras GTPase-activating protein-binding protein Q9UN86 G3BP2 2 (G3BP-2) (GAP SH3 domain-binding protein 482 FALSE FALSE FALSE FALSE FALSE TRUE 2) Ras GTPase-activating-iike protein IQGAP1 QGAP1 1657 FALSE FALSE FALSE FALSE FALSE FALSE (p195) Q13576 IQGAP2 Ras GTPase-activating-iike protein IQGAP2 1575 FALSE FALSE FALSE FALSE FALSE FALSE Ras-related C3 botuiinum toxin substrate 1 Ρ63000 RAC1 (Ceil migration-inducing gene 5 protein) (Ras- 192 FALSE FALSE FALSE FALSE FALSE FALSE ike protein TC25) (p21-Rad) Ras-related C3 botu!inum toxin substrate 2 Ρ 15153 RAC2 Ί FALSE FALSE FALSE FALSE FALSE FALSE (GX) (Small G protein) (p21-Rac2) Ras-related protein R-Ras2 (Ras-like protein Ρ62070 RRAS2 204 FALSE FALSE FALSE FALSE FALSE FALSE TC21) (Teratocarcinoma oncogene) Ρ61026 RAB10 Ras-related protein Rab-10 200 FALSE FALSE FALSE FALSE FALSE FALSE Ras-related protein Rab-1 1B (GTP-binding Q15907 RAB1 1B 218 FALSE FALSE FALSE FALSE FALSE FALSE protein YPT3) P6 Q6 RAB14 Ras-related protein Rab-14 215 TRUE TRUE FALSE FALSE FALSE FALSE Ras-related protein Rab-1A (YPT1-related Ρ62820 RAB1A 205 FALSE FALSE FALSE FALSE FALSE FALSE protein) Q9H0U4 RAB1 B Ras-related protein Rab-1 B 201 FALSE FALSE FALSE FALSE FALSE FALSE Q9UL25 RAB21 Ras-related protein Rab-21 225 FALSE FALSE FALSE TRUE TRUE TRUE Ρ61019 RAB2A Ras-related protein Rab-2A 212 FALSE FALSE FALSE FALSE FALSE FALSE Ras-related protein Rab-35 (GTP-binding Q15286 RAB35 201 FALSE FALSE FALSE FALSE FALSE FALSE protein RAY) (Ras-related protein Rab-1C) Ρ ο 20339 RAB5A Ras-related protein Rab-5A 215 FALSE FALSE FALSE FALSE FALSE FALSE -4 Ρ61020 RAB5B Ras-related protein Rab-5B 215 FALSE FALSE FALSE FALSE FA LS FALSE

P51 148 RAB5C Ras-related protein Rab-5C (L1 880) (RAB5L) 216 F S ! FALSE! FALSE FALSE FALSE FALSE P20340 RAB6A Ras-related protein Rab-6A (Rab-6) 208 FALSE FALSE FALSE FALSE FA LS FALSE P51 149 RAB7A Ras-related protein Rab-7a 207 FALSE FALSE FALSE FALSE FALSE FALSE

P61006 RAB8A Ras-related protein Rab-8A (Oncogene c-mel) 2 7 F ! FALSE! FALSE FALSE FALSE FALSE

Ras-related protein Rap-1A (C21 KG) (G-22K) Ρ62834 RAP1A (GTP-binding protein s n g p21A) (Ras-related 184 FALSE FALSE FALSE TRUE TRUE FALSE protein Krev-1) Ras-related protein Rap-1b (GTP-binding Ρ61224 184 FALSE FA L E FA L FALSE FALSE protein smg p21 B) Q9Y3L5 RAP2C Ras-related protein Rap-2c 183 TRUE FALSE FALSE FALSE FALSE FALSE Receptor of activated protein C kinase 1 (Ce i proliferation-inducing gene 2 1 protein) (Guanine nucleotide-binding protein subunit beta~2~iike 1) (Guanine nucleotide-binding protein subunit beta-like protein 12.3) (Human lung cancer oncogene 7 protein) (HLC-7) P63244 RACK1 3 17 FALSE FALSE FALSE FALSE FALSE FALSE (Receptor for activated C kinase) (Small ribosoma! subunit protein RACK1 ) [Cleaved into: Receptor of activated protein C kinase 1, N-terminally processed (Guanine nucleotide- binding protein subunit beta-2-iike 1, N- terminally processed)]

Receptor-type tyrosine-protein phosphatase C P08575 PTPRC (EC 3 .1.3.48) (Leukocyte common antigen) (L- 1304 FALSE FALSE FALSE FALSE FALSE FALSE CA) (T200) (CD antigen CD45)

Regulation of nuclear pre-mRNA domain- o Q9NQG5 RPRD1 B containing protein 1B (Cell cycle-related and 326 TRUE FALSE FALSE FALSE FALSE TRUE expression-elevated protein in tumor) Regulator of chromosome condensation (Cell P 18754 RCC1 cycle regulatory protein) (Chromosome 42 1 FALSE FALSE FALSE FALSE FALSE FALSE condensation protein 1) Regulator of microtubule dynamics protein 3 (RMD-3) (hRMD-3) (Cerebral protein 1 ) Q96TC7 RMDN3 (Protein FAM82A2) (Protein FAM82C) (Protein 470 FALSE FALSE FALSE FALSE FALSE FALSE tyrosine phosphatase-interacting protein 5 1) (TCPTP-interacfing protein 5 1)

Regulator of nonsense transcripts 1 (EC 3.6.4.- ) (ATP-dependent helicase RENT1 ) Q92900 UPF1 1129 FALSE FALSE FALSE TRU E TRUE TRUE (Nonsense mRNA reducing factor 1) (NORF1 ) (Up-frameshift suppressor 1 homolog) (hUpfl ) Regulator of nonsense transcripts 3B (Nonsense mRNA reducing factor 3B) (Up- Q9BZI7 UPF3B frameshift suppressor 3 homolog B) (hUpfSB) 483 FALSE FALSE FALSE FALSE FALSE FALSE (Up-frameshift suppressor 3 homo!og on chromosome X) (hUpf3p-X)

Replication factor C subunit 1 (Activator 1 140 kDa subunit) (A1 140 kDa subunit) (Activator 1 large subunit) (Activator 1 subunit 1) (DNA- P35251 RFC1 1148 FALSE FALSE TRUE FALSE FALSE FALSE binding protein PO-GA) (Replication factor C 140 kDa subunit) (RF-C 140 kDa subunit) (RFC140) (Replication factor C large subunit)

Replication factor C subunit 2 (Activator 1 40 kDa subunit) (A1 40 kDa subunit) (Activator 1 P35250 RFC2 354 FALSE FALSE FALSE FALSE FALSE FALSE subunit 2) (Replication factor C 40 kDa subunit) (RF-C 40 kDa subunit) (RFC40)

Replication factor C subunit 3 (Activator 1 38 kDa subunit) (A1 38 kDa subunit) (Activator 1 P40938 RFC3 356 TRUE TRUE TRUE TRUE TRUE TRUE subunit 3) (Replication factor C 38 kDa subunit) (RF-C 38 kDa subunit) (RFC38)

Replication factor C subunit 4 (Activator 1 37 kDa subunit) (A1 37 kDa subunit) (Activator 1 P35249 RFC4 363 FALSE FALSE FALSE FALSE TRUE FALSE subunit 4) (Replication factor C 37 kDa subunit) (RF-C 37 kDa subunit) (RFC37)

Replication factor C subunit 5 (Activator 1 36 kDa subunit) (A1 36 kDa subunit) (Activator 1 P40937 RFC5 340 FALSE TRUE FALSE TRUE TRUE TRUE subunit 5) (Replication factor C 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36) Replication initiator 1 (80 kDa origin-specific DNA-binding protein) (60 kDa replication Q9BWE0 REPIN1 initiation region protein) (ATT-binding protein) 567 FALSE FALSE FALSE FALSE FALSE FALSE (DHFR oribeta-binding protein RIP60) (Zinc finger protein 464) Replication protein A 4 kDa subunit (RP-A P35244 RPA3 p14) (Replication factor A protein 3) (RF-A 121 TRUE FALSE FALSE FALSE FALSE FALSE protein 3) Replication protein A 32 kDa subunit (RP-A p32) (Replication factor A protein 2) (RF-A P15927 RPA2 270 FALSE FALSE FALSE TRUE FALSE FALSE protein 2) (Replication protein A 34 kDa subunit) (RP-A p34) Replication protein A 70 kDa DNA-binding subunit (RP-A p70) (Replication factor A protein 1) (RF-A protein 1) (Single-stranded Ρ27694 RPA1 616 TRUE TRUE TRUE FALSE FALSE FALSE DNA-binding protein) [Cleaved into: Replication protein A 70 kDa DNA-binding subunit, N-terminally processed] Q9UKL0 RCOR1 REST corepressor 1 (Protein CoREST) 482 TRUE TRUE FALSE FALSE FALSE FALSE Reticulocalbin-2 (Calcium-binding protein ERC- Q14257 RCN2 317 FALSE FALSE FALSE FALSE FALSE FALSE 55) (E6-binding protein) (E6BP) Reticulon-4 (Foocen) (Neurite outgrowth inhibitor) (Nogo protein) (Neuroendocrine- Q9NQC3 RTN4 specific protein) (NSP) (Neuroendocrine- 1192 FALSE FALSE FALSE FALSE FALSE FALSE specific protein C homo!og) (RTN-x) (Reticulon-5) Retinol dehydrogenase 11 (EC 1 1 . 1 .300) (Androgen-regulated short-chain dehydrogenase/reductase 1) (HCV core- binding protein HCBP12) (Prostate short-chain Q8TC12 RDH1 1 8 FALSE FALSE FALSE FALSE FALSE FALSE dehydrogenase/reductase 1) (Retinal reductase 1) (RalR1) (Short chain dehydrogenase/reductase family 7C member 1) Rho GDP-dissociation inhibitor 1 (Rho GDI 1) Ρ52565 ARHGDIA 204 FALSE FALSE FALSE FALSE FALSE FALSE (Rho-GDI alpha) Rho GTPase-aciivating protein 1 (CDC42 GTPase-activating protein) (GTPase- ARHGAP activating protein rhoGAP) (Rho-related small 439 TRUE FALSE FALSE FALSE TRUE FALSE GTPase protein activator) (Rho-type GTPase- activating protein 1) (p50-RhoGAP)

Rho guanine nucleotide exchange factor 1 ARHGEF Q92888 ' " ' ( 5 kDa guanine nucleotide exchange factor) 912 TRUE TRUE FALSE FALSE FALSE FALSE (p1 15-RhoGEF) (p1 15RhoGEF) (Sub1 .5)

Rho guanine nucleotide exchange factor 2 ARHGEF (Guanine nucleotide exchange factor H1) Q92974 986 TRUE FALSE FALSE F L FALSEi FALSE 2 (GEF-H1) (Microtubule-regulated Rho-GEF) (Proliferating cell nucleolar antigen p40)

Rho-related GTP-binding protein RhoB (Rho P62745 RHOB 196 FALSE FALSE! FALSE FALSE FA LS cDNA clone 6) (h6) P84095 RHOG Rho-related GTP-binding protein RhoG 191 FALSE FALSE FALSE FALSE FALSE FALSE

Riboflavin kinase (EC 2./. 1.26) (ATPxibofiavin Q969G6 155 FALSE FALSE FALSE FALSE FALSE FALSE 5-phosphotransferase) (Flavokinase)

Ribonudease H2 subunif C (RNase H2 RNASEH subunif C) (Aicardi-Goufieres syndrome 3 Q8TDP1 164 FALSE FALSE FALSE FALSE FALSE TRUE 2C protein) (AGS3) (RNase H 1 small subunit) (Ribonudease Hi subunit C)

Ribonudease inhibitor (Placental ribonudease P13489 RNH1 inhibitor) (Placental RNase inhibitor) 461 FALSE FALSE FALSE FALSE FALSE FALSE (Ribonudease/angiogenin inhibitor 1) (RAi) Ribonucieoprofein PTB-binding 1 (Protein Q8IY67 RAVER1 606 FALSE FALSE FALSE FALSE FALSE FALSE raver- 1)

Ribonucieoside-diphosphate reductase large subunif (EC 1.17.4.1) (Ribonucieoside- P23921 RRM1 792 FALSE FALSE FALSE FALSE FALSE FALSE diphosphate reductase subunit M1) (Ribonucleotide reductase large subunit) Ribonudeoside-diphosphaie reductase subunit 2 (EC 1.17.4 1) (Ribonucleotide P31350 RRM2 389 FALSE FALSE FALSE TRUE TRUE FALSE reductase small chain) (Ribonucleotide reductase small subunit) Ribose-phosphate pyrophosphokinase 1 (EC P60891 PRPS1 2.7.6.1) (PPRibP) (Phosphoribosyl 318 FALSE FALSE FALSE FALSE TRUE TRUE pyrophosphate synthase ) (PRS-I) Ribosomal biogenesis protein LAS1 L (Protein Q9Y4W2 LAS1 L 734 FALSE FALSE FALSE FALSE FALSE FALSE LAS1 homolog) Ribosomal L 1 domain-containing protein 1 076021 RSL1 D 1 (CATX-1 1) (Cellular senescence-inhibited 490 FALSE FALSE FALSE FALSE FALSE FALSE gene protein) (Protein PBK1) Ribosomal RNA processing protein 1 homolog P56182 RRP1 A (Novel nuclear protein 1) (NNP-1) (Nucleolar 461 FALSE FALSE FALSE FALSE FALSE FALSE protein Nop52) (RRP1~like protein)

Ribosomal RNA processing protein 1 homolog Q14684 RRP1 B 758 FALSE FALSE FALSE TRUE TRUE TRUE B (RRP1-like protein B) Ribosomal RNA small subunit methyltransferase NEP1 (EC 2.1.1 .-) (18S rRNA (pseudouridine(1248)-N1)~ Q92979 E G 1 methyltransferase) (18S rRNA Psi1248 244 FALSE TRUE FALSE FALSE FALSE FALSE methyltransferase) (Nucleolar protein EMG1 homolog) (Protein C2f) (Ribosome biogenesis protein NEP1)

Ribosomal RNA-processing protein 8 (EC 043159 RRP8 456 FALSE FALSE FALSE FALSE FALSE FALSE 2.1 . 1 .-) (Cerebral protein 1) (Nucleomefhylin)

Ribosome biogenesis protein B S1 homolog Q14692 BMS1 1282 FALSE FALSE FALSE FALSE FALSE FALSE (Ribosome assembly protein B S 1 homolog)

Ribosome biogenesis protein BOP1 (Block of Q14137 BOP1 746 FALSE FALSE FALSE TRUE TRUE TRUE proliferation 1 protein)

Ribosome biogenesis protein BRX1 homolog Q8TDN6 BRIX1 353 FALSE FALSE FALSE TRUE TRUE TRUE (Brix domain-containing protein 2) Ribosome biogenesis protein WDR1 2 (WD Q9GZL7 WDR1 2 423 FALSE FALSE TRUE TRUE TRUE TRUE repeat-containing protein 12)

Ribosome production factor 2 homolog (Brix Q9H7B2 RPF2 domain-containing protein 1) (Ribosome 306 FALSE TRUE TRUE FALSE FALSE FALSE biogenesis protein RPF2 homolog)

Ribosome-binding protein 1 ( 180 kDa Q9P2E9 RRBP1 ribosome receptor homolog) (RRp) (ES/1 30- 14 10 FALSE FALSE FALSE FALSE FALSE FALSE related protein) (Ribosome receptor protein)

RNA 3'-ferminal phosphate cyclase-like Q9Y2P8 RCL1 373 FALSE FALSE FALSE FALSE FALSE FALSE protein RNA cytidine acetyltransferase (EC 2.3. 1.-) Q9H0A0 AT 10 ( 18S rRNA cytosine acetyltransferase) (N- 1 25 FALSE FALSE FALSE ∆ FALSE acetyltransferase 10) RNA demethylase ALKBH5 (EC 1.14 .11.-) (Alkylated DNA repair protein a kB homolog 5) Q6P6C2 ALKBH5 394 FALSE S F FALSE TRUE TRUE (Alpha-ketoglutarate-dependent dioxygenase alkB homolog 5) Q9BWH6 RPAP1 RNA polymerase l~associated protein 1 1393 FALSE FALSE FALSE FALSE FALSE FALSE RNA-binding motif proiein, X chromosome (Glycoprotein p43) (Heterogeneous nuclear P381 59 RB X ribonudeoprotein G) (hnRNP G) [Cleaved into: 391 FALSE FALSE FALSE FALSE FALSE FALSE RNA-binding motif protein, X chromosome, N- terminaliy processed]

RNA-binding protein 14 (Paraspeckle protein 2) (PSP2) (RNA-binding motif protein 14) Q96PK6 RB 14 (RRM-containing coactivator 669 FALSE FALSE FALSE FALSE FALSE FALSE activator/modulator) (Synaptotagmin- interacting protein) (SYT-interacting proiein)

RNA-binding protein 25 (Arg/Glu/Asp-rich protein of 120 kDa) (RED1 20) (Protein S 164) P49756 RB 25 843 FALSE FALSE FALSE TRU E TRUE TRUE (RNA-binding motif protein 25) (RNA-binding region-containing proiein 7) RNA-binding protein 28 (RNA-binding motif Q9NW13 RB 28 759 FALSE FALSE FALSE FALSE TRUE FALSE protein 28) RNA-binding protein 34 (RNA-binding motif P42696 RB 34 430 FALSE FALSE FALSE FALSE FALSE FALSE protein 34)

RNA-binding protein 39 (CAPER alpha) (Hepatocellular carcinoma protein 1) (RNA- Q14498 RBM39 530 FALSE FALSE FALSE FALSE FALSE FALSE binding motif protein 39) (RNA-binding region- containing protein 2) (Splicing factor HCC1) RNA-binding protein 4 (Lark homolog) (hLark) Q9BWF3 RB 4 (RNA-binding motif protein 4) (RNA-binding 364 FALSE FALSE FALSE FALSE FALSE FALSE motif protein 4a) RNA-binding protein 42 (RNA-binding motif Q9BTD8 RB 42 480 FALSE TRUE FALSE FALSE FALSE FALSE protein 42) RNA-binding protein 8A (Binder of OVCA1-1) (BOV-1) (RNA-binding motif protein 8A) (RNA- Q9Y5S9 RB 8A 174 FALSE FALSE FALSE FALSE FALSE FALSE binding protein Y14) (Ribonucleoprotein RB 8A) RNA-binding protein EWS (EWS oncogene) QQ1 844 EWSR1 656 FALSE FALSE FALSE FALSE FALSE FALSE (Ewing sarcoma breakpoint region 1 protein) RNA-binding protein FUS (75 kDa DNA- pairing protein) (Oncogene FUS) (Oncogene P35637 FUS 526 FALSE FALSE FALSE FALSE FALSE FALSE TLS) (POMp75) (Translocated in liposarcoma protein)

RNA-binding protein NOB1 (Phosphorylation Q9ULX3 NOB1 412 FALSE FALSE FALSE FALSE FALSE FALSE regulatory protein HP-10) (Protein ART-4) G9NRX1 PN01 RNA-binding protein PN01 252 FALSE FALSE FALSE FALSE FALSE FALSE

RNA-binding protein Ra y (Autoantigen p542) (Heterogeneous nuclear ribonucleoprotein C- Q9UK 9 RALY 3 6 FALSE FALSE FALSE FALSE FALSE FALSE ike 2) (hnRNP core protein C-like 2) (hnRNP associated with lethal yellow protein homolog) RNA-binding protein with serine-rich domain 1 Q15287 RNPS1 305 FALSE FALSE FALSE FALSE FALSE FALSE (SR-related protein LDC2) rRNA 2'-0-methyiiransferase fibrillarin (EC 2.1 . 1 .-) (34 kDa nucleolar scleroderma P22087 FBL 321 FALSE FALSE FALSE FALSE FALSE FALSE antigen) (Histone-giuiamine methyltransferase) Q5JTH9 RRP12 RRP12-!ike protein 1297 FALSE FALSE FALSE FALSE FALSE FALSE RRP15-like protein (Ribosomal RNA- Q9Y3B9 RRP15 282 FALSE FALSE FALSE TRUE FALSE FALSE processing protein 15) Q96GQ5 C16orf58 RUS1 family protein C16orf58 468 FALSE FALSE FALSE TRUE FALSE FALSE

RuvB-like 1 (EC 3.6.4.12) (49 kDa TATA box- binding protein-interacting protein) (49 kDa TBP-interacting protein) (54 kDa erythrocyte Q9Y265 RUVBL1 cytosoiic protein) (ECP-54) ( O80 complex 456 TRUE FALSE FALSE TRUE TRUE TRUE subunit H) (Nuclear matrix proiein 238) (NMP 238) (Poniin 52) (T!P49a) (TIP60-associated protein 54-aipha) (TAP54-alpha)

RuvB-like 2 (EC 3 6.4.12) (48 kDa TATA box- binding protein-interacting protein) (48 kDa TBP-interacting proiein) (51 kDa erythrocyte Q9Y230 R.UVBL2 cytosoiic protein) (ECP-51) (INO80 complex 463 TRUE FALSE FALSE FALSE FALSE FALSE subunit J) (Repressing poniin 52) (Repiin 52) (TIP49b) (TiP60-associated protein 54-beta) (TAP54-beta)

S-adenosylmeihionine synthase isoform iype- 2 (AdoMet synthase 2) (EC 2.5.1 .6) Ρ 3 153 T2A 395 FALSE FALSE FALSE FALSE FALSE FALSE (Methionine adenosyltransferase 2) (MAT 2) (Methionine adenosyltransferase II) (MAT- )

S-formylgiutaihione hydrolase (FGH) (EC Ρ 10768 3.1 .2.12) (Esterase D) (Methylumbeliiferyl FALSE FALSE FALSE FALSE FALSE FALSE acetate deacetylase) (EC 3.1 . 1 .56) S-phase kinase-associated protein 1 (Cyclin- A/CDK2-associated protein p19) (p19A) (Organ of Corti protein 2) (OCP-2) (Organ of P63208 SKP1 Corti protein II) (OCP-I!) (RNA polymerase II 163 FALSE TRUE FALSE FALSE FALSE FALSE elongation factor-like protein) (Sill) (Transcription elongation factor B polypeptide 1-like) (p19skp1) Saccharopine dehydrogenase-like Q8NBX0 SCCPDH 429 TRUE FALSE FALSE FALSE FALSE FALSE oxidoreductase (EC .-.-.-) SAP domain-containing ribonucleoprotein (Cytokine-induced protein of 29 kDa) (Nuclear P82979 SARNP 210 TRUE FALSE FALSE FALSE FALSE FALSE protein Hcc-1) (Proliferation-associated cytokine-inducible protein CIP29) Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) (SR Ca(2÷)-ATPase 2) (EC 3.6.3.8) (Calcium pump 2) (Caicium- Ρ 16615 ATP2A2 transporting ATPase sarcoplasmic reticulum FALSE FALSE FALSE TRUE TRUE TRUE type, slow twitch skeletal muscle isoform) (Endoplasmic reticulum class 1/2 Ca(2+) ATPase) Sarcoplasmic/endoplasmic reticulum calcium Q93084 ATP2A3 ATPase 3 (SERCA3) (SR Ca(2+)-ATPase 3) 3 FALSE FALSE FALSE FALSE FALSE FALSE (EC 3.6.3.8) (Calcium pump 3) Scaffold attachment factor B 1 (SAF-B) (SAF- B1) (HSP27 estrogen response e!ement-TATA Q15424 SAFB 915 FALSE FALSE FALSE FALSE FALSE FALSE box-binding protein) (HSP27 ERE-TATA- binding protein) Q14151 SAFB2 Scaffold attachment factor B2 (SAF-B2) 953 TRUE FALSE FALSE FALSE FALSE FALSE Sec1 family domain-containing protein 1 G8WV 8 (SLY1 homoiog) (Siylp) (Syntaxin-binding 642 TRUE FALSE FALSE FALSE TRUE FALSE protein 1-like 2) Secretory carrier-associated membrane 015127 SCA P2 protein 2 (Secretory carrier membrane protein 329 FALSE FALSE FALSE TRUE TRUE TRUE 2) Secretory carrier-associated membrane 014828 SCAMPS protein 3 (Secretory carrier membrane protein 347 FALSE FALSE FALSE FALSE FALSE FALSE 3) Sentrin-specific protease 3 (EC 3.4.22 68) Q9H4L4 SENP3 (SUMO-1 -specific protease 3) (Sentrin/SUMO- 574 FALSE TRUE FALSE FALSE FALSE FALSE specific protease SENP3)

P35270 SPR Sepiapterin reductase (SPR) (EC 1. 1 . 1 .153) 261 FALSE FALSE FALSE FALSE FALSE FALSE

Q9NVA2 42989 Septin-1 1 429 FALSE FALSE FALSE FALSE FALSE FALSE Septin-2 (Neural precursor ceil expressed Q15019 42980 developmentally down-regulated protein 5) 361 FALSE FALSE FALSE FALSE FALSE FALSE (NEDD-5) Q14141 42984 Septin-6 434 TRUE FALSE FALSE FALSE FALSE Q16181 42985 Septin-7 (CDC10 protein homolog) 437 FALSE FALSE FALSE FALSE F LS E FALSE Septin-9 ( LL septin-like fusion protein SF- A) (MLL septin-like fusion protein) Q9UHD8 42987 586 F S ! FALSE FALSE! FA S . FALSE FALSE (Ovarian/Breast septin) (Ov/Br septin) (Septin D1)

Serine hydroxymethyltransferase, cytosolic P34896 SH T 1 (SH T) (EC 2.1 .2.1) (Glycine 483 FALSE FALSE FALSE FALSE FALSE FALSE hydroxymethyltransferase) (Serine methylase)

Serine hydroxymethyltransferase, P34897 SHMT2 mitochondrial (SHMT) (EC 2.1 .2 1) (Glycine 504 FALSE FALSE FALSE FALSE FALSE FALSE hydroxymethyltransferase) (Serine methylase)

Serine palmitoyltransferase 1 (EC 2 3 1.50) (Long chain base biosynthesis protein 1) (LCB 015269 SPTLC1 473 TRUE TRUE TRUE FALSE TRUE TRUE 1) (Serine-palmitoyl-CoA transferase 1) (SPT 1) (SPT1) Serine palmitoyltransferase 2 (EC 2.3.1 .50) (Long chain base biosynthesis protein 2) (LCB 2 2) (Long chain base biosynthesis protein 2a) (LCB2a) (Serine-palmitoyi-CoA transferase 2) (SPT 2) Serine-tRNA ligase, cytoplasmic (EC P49591 SARS 6.1 . 1 . 1 1) (Seryi-tRNA synthetase) (SerRS) 514 FALSE FALSE FALSE FALSE FALSE FALSE (Seryl-tRNA(Ser/Sec) synthetase)

Serine-tRNA ligase, mitochondrial (EC Q9NP81 SARS2 6.1 . 1 . 1 1) (SerRSmt) (Seryi-tRNA synthetase) 518 FALSE FALSE FALSE FALSE FALSE FALSE (SerRS) (Seryi-tRNA(Ser/Sec) synthetase) Serine-threonine kinase receptor-associated protein (MAP activator with W D repeats) (UNR- Q9Y3F4 STRAP 350 F L3 Ε A Ξ F L F Ε FA Ξ FAL EE interacting protein) (WD-40 repeat protein PT- WD) Serine/arginine repetitive matrix protein 1 (SR- related nuclear matrix protein of 160 kDa) Q8IYB3 SRRM1 9 4 FALSE FALSE FALSE FALSE FALSE FALSE (SRm160) (Ser/Arg-related nuclear matrix protein)

Serine/arginine repetitive matrix protein 2 (300 kDa nuclear matrix antigen) (Serine/arginine- oe rich splicing factor-related nuclear matrix protein of 300 kDa) (SR-related nuclear matrix Q9UQ35 SRR 2 protein of 300 kDa) (Ser/Arg-related nuclear 2752 FALSE FALSE FALSE FALSE FALSE FALSE matrix protein of 300 kDa) (Splicing coactivator subunit SRm300) (Tax-responsive enhancer element-binding protein 803) (TaxREB803)

Serine/arginine-rich splicing factor 1 (Alternative-splicing factor 1) (ASF-1) (Splicing Q07955 SRSF1 248 FALSE FALSE FALSE FALSE FALSE FALSE factor, arginine/serine-rich 1) (pre-mRNA- spiicing factor SF2, P33 subunit) Serine/arginine-rich splicing factor 0 (40 kDa SR-repressor protein) (SRrp40) (FUS- interacting serine-arginine-rich protein 1) (Splicing factor SRp38) (Splicing factor, 075494 SRSF10 arginine/serine-rich 13A) (TLS-associated 262 FALSE FALSE FALSE FALSE FALSE FAL protein with Ser-Arg repeats) (TASR) (TLS- associated protein with SR repeats) (TLS- associated serine-arginine protein) (TLS- associated SR protein) Serine/arginine-rich splicing factor 1 Q05519 SRSF1 1 (Arginine-rich 54 kDa nuclear protein) (p54) 484 FALSE FALSE FALSE FALSE FALSE FALSE (Splicing factor, arginine/serine-rich 11) Serine/arginine-rich splicing factor 2 (Protein PR264) (Splicing component, 35 kDa) Q01 130 SRSF2 22 FALSE! FALSE FALSE! FALSE FALSE! FALSE (Splicing factor SC35) (SC-35) (Splicing factor, arginine/serine-rich 2)

» Serine/arginine-rich splicing factor 3 (Pre- P84103 SRSF3 mRNA-splicing factor SRP20) (Splicing factor, 164 FALSE FALSE FALSE FALSE FALSE FALSE arginine/serine-rich 3) Serine/arginine-rich splicing factor 4 (Pre- Q081 0 SRSF4 mRNA-splicing factor SRP75) (SRP001 LB) 494 FALSE FALSE FALSE FALSE FALSE FALSE (Splicing factor, arginine/serine-rich 4)

Serine/arginine-rich splicing factor 5 (Delayed- Q13243 SRSF5 early protein HRS) (Pre-mRNA-splicing factor 272 FALSE FALSE FALSE FALSE FALSE FALSE SRP40) (Splicing factor, arginine/serine-rich 5) Serine/arginine-rich splicing factor 6 (Pre- Q13247 SRSF6 mRNA-splicing factor SRP55) (Splicing factor, 344 FALSE FALSE FALSE FALSE FALSE FALSE arginine/serine-rich 6) Serine/arginine-rich splicing factor 7 (Splicing Q16629 SRSF7 factor 9G8) (Splicing factor, arginine/serine- 23B FA LS E! F E FA LS ! rich 7) Serine/arginine-rich splicing factor 9 (Pre- Q13242 SRSF9 mRNA-sp!icing factor SRp30C) (Splicing 221 FALSE FALSE FALSE FALSE FALSE FALSE factor, arginine/serine-rich 9) Serine/threonine-protein kinase 26 (EC 2.7.1 1.1) ( ST3 and SOK1 -related kinase) Q9P289 STK26 (Mammalian STE20-like protein kinase 4) FALSE FALSE FALSE TRUE FALSE FALSE (MST-4) (STE20-iike kinase ST4) (Serine/threonine-protein kinase MASK)

Serine/threonine-protein kinase N 1 (EC 2.7.1 1.13) (Protease-activated kinase 1) (PAK- 1) (Protein kinase C-like 1) (Protein kinase C- Q16512 ΡΚΝ 1 942 FALSE FALSE FALSE TRUE TRUE TRUE ike PKN) (Protein kinase PKN-alpha) (Protein- kinase C~related kinase 1) (Serine-threonine protein kinase N) Serine/threonine-protein kinase OSR1 (EC 095747 OXSR1 2.7.1 1.1) (Oxidative stress-responsive 1 527 FALSE FALSE FALSE FALSE FALSE FALSE protein) ο Serine/threonine-protein kinase PAK 2 (EC 2.7.1 1.1) (Gamma-PAK) (PAK65) (S6/H4 Q13177 PAK2 kinase) (p21 -activated kinase 2) (PAK-2) (p58) 524 FALSE FALSE FALSE FALSE FALSE FALSE [Cleaved into: PAK-2p27 (p27); PAK-2p34 (p34) (C-t-PAK2)] Serine/threonine-protein kinase PRP4 Q13523 PRPF4B homolog (EC 2.7.1 1.1) (PRP4 kinase) (PRP4 1007 FALSE FALSE FALSE FALSE FALSE FALSE pre-mRNA-processing factor 4 homolog)

Serine/threonine-protein kinase TBK1 (EC Q9UHD2 TBK1 2.7.1 1.1) (NF-kappa-B-activating kinase) 729 FALSE FALSE FALSE FALSE FALSE FALSE (T2K) (TANK-binding kinase 1) Serine/threonine-protein kinase VRK1 (EC Q99986 VRK1 396 FALSE FALSE FALSE FALSE FALSE FALSE 2.7.1 1.1) (Vaccinia-related kinase 1) Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A PPP2R2A subunit B isoform B55-alpha) (PP2A subunit B 447 FALSE FALSE FALSE TRUE TRUE TRUE isoform PR55-aipha) (PP2A subunit B isoform R2-aipha) (PP2A subunit B isoform alpha)

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform P30153 PPP2R1A (Medium tumor antigen-associated 6 1 kDa 589 FALSE FALSE FALSE FALSE FALSE FALSE protein) (PP2A subunit A isoform PR65-aipha) (PP2A subunit A isoform R 1-alpha) Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform (PP2A P30154 PPP2R1B 6 1 TRUE TRUE TRUE TRUE FALSE TRUE subunit A isoform PR65-beta) (PP2A subunit A isoform R1-beta)

Serine/threonine-protein phosphatase 2A activator (EC 5.2.1 .8) (PP2A, subunit B', PR53 isoform) (Phosphotyrosyl phosphatase Q15257 PTPA activator) (PTPA) (Serine/threonine-protein 358 FALSE FALSE FALSE TRUE FALSE FALSE phosphatase 2A regulatory subunit 4) (Serine/threonine-protein phosphatase 2A regulatory subunit B')

Serine/threonine-protein phosphatase 2A P67775 PPP2CA catalytic subunit alpha isoform (PP2A-alpha) 309 FALSE FALSE FALSE FALSE FALSE FALSE (EC 3.1 .3.16) (Replication protein C) (RP-C) Serine/threonine-protein phosphatase 5 (PP5) P53041 PPP5C (EC 3.1 .3.16) (Protein phosphatase T) (PP-T) 499 FALSE FALSE FALSE TRUE TRUE FALSE (PPT) Serine/threonine-protein phosphatase 6 catalytic subunit (PP6C) (EC 3.1 .3.16) 000743 PPP6C [Cleaved into: Serine/threonine-protein 305 FALSE FALSE FALSE TRUE FALSE TRUE phosphatase 6 catalytic subunit, N-terminally processed] Serine/threonine-proiein phosphatase 6 regulatory ankyrin repeat subunit A (PP6-ARS A) (Serine/threonine-protein phosphatase 6 015084 1053 FALSE FALSE FALSE FALSE FALSE TRUE regulatory subunit ARS-A) (Ankyrin repeat domain-containing protein 28) (Phosphatase interactor targeting protein hnRNP K) (PITK) Serine/threonine-protein phosphatase PGAM5, mitochondrial (EC 3.1 .3.16) (Bcl-XL- Q96HS1 PGA 5 289 FALSE FALSE FALSE TRUE TRUE FALSE binding protein v68) (Phosphogiycerate mutase family member 5)

Serine/threonine-protein phosphatase PP1- P62136 PPP1CA 330 TRUE TRUE FALSE FALSE FALSE FALSE a pha catalytic subunit (PP-1 A) (EC 3.1 .3.16) Serine/threonine-protein phosphatase PP1- P62140 PPP1 CB beta catalytic subunit (PP-1 B) (PPP1 CD) (EC 327 FALSE FALSE FALSE FALSE FALSE FALSE 3.1 .3.16) (EC 3.1 .3.53) Serrate RNA effector molecule homoiog Q9BXP5 SRRT 876 FALSE FALSE FALSE FALSE FALSE FALSE (Arsenite-resistance protein 2) Set1/Ash2 histone methyltransferase complex Q9UBL3 ASH2L 628 TRUE FALSE FALSE TRUE FALSE FALSE subunit ASH2 (ASH2-like protein) Q9UQR0 SC L2 Sex comb on midleg-!ike protein 2 700 FALSE FALSE FALSE FALSE FALSE FALSE

Sialic acid synthase (N-acetylneuraminate synthase) (EC 2.5.1 .56) (N-acetylneuraminate- Q9NR45 NANS 9-phosphate synthase) (EC 2.5 1.57) (N- 359 FALSE FALSE FALSE FALSE FALSE FALSE acetylneuraminic acid phosphate synthase) (N- acetylneuraminic acid synthase) Sideroflexin-1 (Tricarboxylate carrier protein) Q9H9B4 SFXN1 322 FALSE FALSE FALSE FALSE FALSE FALSE (TCC) Signal peptidase complex catalytic subunit SEC1 1A (EC 3.4.21 .89) (Endopeptidase ;C1 1A SP18) (Microsomal signal peptidase 18 kDa 179 TRUE TRUE FALSE FALSE FALSE FALSE subunit) (SPase 18 kDa subunit) (SEC1 1 homoiog A) (SEC1 1-iike protein 1) (SPC18) Signal peptidase complex subunit 1 (EC 3.4.-.- Q9Y6A9 SPCS1 ) (Microsomal signal peptidase 12 kDa 102 TRUE TRUE FALSE FALSE TRUE TRUE subunit) (SPase 12 kDa subunit) Signal peptidase complex subunit 2 (EC 3.4.-.- Q15005 SPCS2 ) (Microsomal signal peptidase 25 kDa 226 FALSE FALSE FALSE FALSE FALSE FALSE subunit) (SPase 25 kDa subunit) Signal peptidase complex subunit 3 (EC 3.4.-.- ) (Microsomal signal peptidase 22/23 kDa Ρ61009 SPCS3 180 FALSE FALSE FALSE FALSE FALSE FALSE subunit) (SPC22/23) (SPase 22/23 kDa subunit) Signal recognition particle 14 kDa protein P371G8 SRP14 136 TRUE FALSE TRUE FALSE FALSE FA LS (SRP14) (18 kDa Alu RNA-binding protein) Signal recognition particle 19 kDa protein Ρ09132 SRP19 144 FALSE FALSE TRUE TRUE TRUE TRUE (SRP19) Signal recognition particle 54 kDa protein Ρ6101 1 SRP54 5 4 FALSE FALSE! FALSE FALSE FA LS (SRP54) Signal recognition particle 9 kDa protein Ρ49458 SRP9 86 FALSE F LS E FALSE! FALSE FALSE FALSE (SRP9) Signal recognition particle receptor subunit Ρ08240 SRPRA alpha (SR~alpha) (Docking protein alpha) (DP- 638 FALSE FALSE FALSE FALSE FALSE TRUE alpha) Signal recognition particle receptor subunit Q9Y5 8 SRPRB 271 FALSE FALSE ALSE FALSE FALSE FALSE beta (SR-beta) (Protein APMCF1) Signal recognition particle subunit SRP68 Q9UHB9 SRP68 (SRP68) (Signal recognition particle 68 kDa 627 FALSE FALSE FALSE FALSE FALSE FALSE protein) Signal recognition particle subunit SRP72 076094 SRP72 (SRP72) (Signal recognition particle 72 kDa 671 FALSE FALSE FALSE TRUE TRUE TRUE protein) Signal transducer and activator of transcription Ρ42224 STAT1 1-alpha/beta (Transcription factor ISGF-3 750 TRUE TRUE FALSE FALSE FALSE FALSE components p91/p84)

Signal iransducer and activator of transcription Ρ40763 STATS 770 FALSE FALSEi FALSE! TRUE TRUE TRUE 3 (Acute-phase response factor) Signal transducer and activator of transcription P51692 STATSB 787 TRUE TRUE FALSE FALSE FALSE FALSE 5B Single-stranded DNA-binding protein, QQ4837 SSBP1 mitochondrial (Mt-SSB) (MtSSB) (PWP1- 148 FALSE FALSE FALSE TRUE TRUE FALSE interacting protein 17) Sister chromatid cohesion protein PDS5 homolog A (Cell proliferation-inducing gene 54 Q29RF7 PDS5A 1337 FALSE FALSE FALSE FALSE FALSE FALSE protein) (Sister chromatid cohesion protein 112) (SC 112) Sister chromatid cohesion protein PDS5 homolog B (Androgen-induced proliferation Q9NTI5 PDS5B FALSE FALSE FALSE TRUE TRUE TRUE inhibitor) (Androgen-induced prostate proliferative shutoff-associated protein AS3)

000193 S AP Small acidic protein 183 FALSE FALSE FALSE FALSE FALSE FALSE Small glutamine-rich tetratricopeptide repeat- 043765 SGTA containing protein alpha (Alpha-SGT) (Vpu- FALSE FALSE FALSE FALSE FALSE FALSE binding protein) (UBP) Small nuclear ribonudeoprotein E (snRNP-E) P62304 SNRPE TRUE TRUE FALSE FALSE FALSE FALSE (Sm protein E) (Sm-E) (SmE) Small nuclear ribonudeoprotein F (snRNP-F) P62306 SNRPF FALSE FALSE FALSE FALSE FALSE FALSE (Sm protein F) (Sm-F) (SmF) Small nuclear ribonudeoprotein Sm D 1 (Sm- P62314 SNRPD1 D1) (Sm-D autoantigen) (snRNP core protein 119 FALSE FALSE FALSE TRUE TRUE FALSE D1) Small nuclear ribonudeoprotein Sm D2 (Sm- P62316 SNRPD2 118 FALSE FALSE FALSE FALSE FALSE FALSE D2) (snRNP core protein D2) Small nuclear ribonudeoprotein Sm D3 (Sm- P62318 SNRPD3 126 FALSE FALSE FALSE FALSE FALSE FALSE D3) (snRNP core protein D3) Small nuclear ribonucleoprotein-associated P14678 SNRPB proteins B and B' (snRNP-B) (Sm protein B/B') FALSE FALSE FALSE FALSE FALSE FALSE (Sm-B/B') (SmB/B') Small subunii processome component 20 homolog (Down-regulated in metastasis 075691 UTP20 2785 FALSE FALSE FALSE FALSE FALSE FALSE protein) (Novel nucleolar protein 73) (NNP73) (Protein Key-1A6) Small ubiquitin-related modifier 2 (SUMO-2) (HSMT3) (SMT3 homolog 2) (SUMO-3) Ρ61956 SU 0 2 95 TRUE FALSE FALSE FALSE FALSE FALSE (Sentrin-2) (Ubiquitin-like protein SMT3B) (SmiSB)

SNW domain-containing protein 1 (Nuclear Q13573 SNW1 protein SkiP) (Nuclear receptor coactivaior 536 FALSE FALSE FALSE FALSE FALSE FALSE NCoA-62) (Ski-interacting protein)

Sodium/potassium-transporting ATPase subunit alpha- 1 (Na(+)/K(+) ATPase alpha- 1 Ρ05023 ΑΤΡ 1Α1 1023 FALSE FALSE! FALSE FALSE FA LS subunit) (EC 3.6.3.9) (Sodium pump subunit alpha-1) Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent Ρ 54709 ΑΤΡ 1Β3 279 TRUE F LS E FALSE! FALSE FALSE FA LS ATPase subunit beta-3) (ATPB-3) (CD antigen CD298) Solute carrier family 22 member 9 (Organic Q 8 V IV 8 SLC22A9 S 3 FALSE FALSE FALSE FALSE FALSE FALSE anion transporter 7) •J\ Something about silencing protein 10 (Charged amino acid-rich leucine zipper 1) Q9NQZ2 UTP3 479 TRUE FALSE FALSE FALSE FALSE FALSE (CRL1) (Disrupter of silencing SAS10) (UTP3 homolog) Sorbitol dehydrogenase (EC 1. 1 . 1 .14) (L-iditoi Q00796 SORD 357 FALSE FALSE FALSE TRUE TRUE TRUE 2-dehydrogenase)

Ρ30626 SRI Sorcin (22 kDa protein) (CP-22) (CP22) (V19) 198 FALSE FALSE FALSE FALSE FALSE FALSE

Sorting and assembly machinery component Q9Y512 SAMMSO 50 homolog (Transformation-related gene 3 469 TRUE TRUE FALSE TRUE FALSE TRUE protein) (TRG-3) Q 13596 SNX1 Sorting nexin-1 522 FALSE FALSE FALSE FALSE FALSE FALSE Sorting nexin-2 (Transformation-related gene 060749 SNX2 519 FALSE TRUE FALSE FALSE FALSE FALSE 9 protein) (TRG-9) Q9Y5X3 SNX5 Sorting nexin-5 404 FALSE FALSE FALSE FALSE FALSE FALSE Spectrin beta chain, non-erythrocytic 1 (Beta-li 001082 SPTBN1 spectrin) (Fodrin beta chain) (Spectrin, non- 2364 TRUE FALSE FALSE FALSE FALSE FALSE erythroid beta chain 1) Sperm-associated antigen 5 (Astrin) (Deepest) Q96R06 SPAG5 (Mitotic spindle-associated protein p126) 1193 FALSE TRUE FALSE FALSE TRUE FALSE (MAPI 26)

Q96SI9 STRBP Spermatid perinuclear RNA-binding protein 672 TRUE FALSE FALSE FALSE TRUE FALSE

SPATA5L Spermatogenesis-associated protein 5-like Q9BVQ7 753 FALSE FALSE FALSE FALSE FALSE FALSE 1 protein 1

Spermidine synthase (SPDSY) (EC 2.5.1.16) Ρ 19623 302 FALSE FALSE FALSE FALSE FALSE TRUE (Putrescine aminopropyitransferase)

Sphingomyelin phosphodiesterase 4 (EC 3.1 .4.12) (Neutral sphingomyelinase 3) Q9NXE4 S PD4 827 FALSE FALSE! FALSE FALSE FA LS (nSMase-3) (nSMaseS) (Neutral sphingomyelinase III) Spiiceosome RNA helicase DDX39B (EC 3.6.4.13) (56 kDa U2AF65-associated protein) Q13838 (ATP-dependent RNA helicase p47) (DEAD 428 FALSE FALSE FALSE TRUE TRUE TRUE box protein UAP56) (HLA~B-associated transcript 1 protein) Spliceosome-associated protein C C15 Q9PQ13 CWC15 229 FALSE FALSE L FALSE FALSE FALSE homoiog

Splicing factor 1 (Mammalian branch point- binding protein) (BBP) (mBBP) (Transcription Q 15637 SF1 639 FALSE FALSE FALSE FALSE FALSE FALSE factor ZFM1) (Zinc finger gene in MEN1 locus) (Zinc finger protein 162)

Splicing factor 3A subunit 1 (SF3a120) Q 15459 SF3A1 (Spliceosome-associated protein 114) (SAP 793 FALSE FALSE FALSE FALSE FALSE FALSE 114)

Splicing factor 3A subunit 2 (SF3a66) Q 15428 SF3A2 464 FALSE FALSE FALSE FALSE FALSE FALSE (Spliceosome-associated protein 62) (SAP 62)

Splicing factor 3A subunit 3 (SF3a60) Q12874 SF3A3 5 1 FALSE FALSEi FALSE! FALSE FALSE FALSE (Spliceosome-associated protein 61) (SAP 61) Splicing factor 3Β subunit 1 (Pre-mRNA- splicing factor SF3b 155 kDa subunit) 075533 SF3B1 TRUE TRUE FALSE FALSE FALSE FALSE (SF3b155) (Spliceosome-associated protein 155) (SAP 155) Splicing factor 3B subunit 2 (Pre-mRNA- splicing factor SF3b 145 kDa subunit) Q13435 SF3B2 TRUE TRUE FALSE TRUE TRUE FALSE (SF3b145) (SF3b150) (Spliceosome- associated protein 145) (SAP 145) Splicing factor 3B subunit 3 (Pre-mRNA- splicing factor SF3b 130 kDa subunit) Q15393 SF3B3 1217 FALSE FALSE FALSE FALSE FALSE FALSE (SF3b130) (STAF130) (Spliceosome- associated protein 130) (SAP 130)

Splicing factor 3B subunit 4 (Pre-mRNA-

Q15427 SF3B4 spiicing factor SF3b 49 kDa subunit) (SF3b50) F L3 Ε A L Ξ F L3 Ε F LS Ε FA L Ξ FA L3 EE (Spliceosome-associated protein 49) (SAP 49)

Splicing factor 3B subunit 5 (SF3b5) (Pre- Q9BWJ5 SF3B5 86 FALSE FALSE FALSE TRUE FALSE TRUE mRNA-splicing factor SF3b 1 kDa subunit) -4 Splicing factor 3B subunit 6 (Pre~mRNA branch site protein p14) (SF3b 14 kDa Q9Y3B4 SF3B6 subunit) (SF3B14a) (Spliceosome-associated 125 FALSE FALSE FALSE FALSE FALSE FALSE protein, 14-kDa) (Splicing factor 3b, subunit 6 , 14kDa) Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 small QQ1081 U2AF1 240 FALSE FALSE FALSE FALSE FALSE FALSE nuclear RNA auxiliary factor 1) (U2 snRNP auxiliary factor small subunit) Splicing factor U2AF 65 kDa subunit (U2 auxiliary factor 65 kDa subunit) (hU2AF(65)) Ρ26368 U2AF2 475 FALSE FALSE FALSE FALSE FALSE FALSE (hU2AF65) (U2 snRNP auxiliary factor large subunit) Splicing factor, arginine/serine-rich 15 (CTD- 095104 SCAF4 binding SR-like protein RA4) (SR-related and 1147 FALSE FALSE FALSE FALSE FALSE FALSE CTD-associated factor 4) Splicing factor, proline- and glutamine-rich (100 kDa DNA-pairing protein) (hPO pl O) (DNA-binding p52/p100 complex, 100 kDa P23246 SFPQ 707 FALSE FALSE FALSE FALSE FALSE FAL subunit) (Polypyrimidine tract-binding protein- associated-spiicing factor) (PSF) (PTB- associated-spiicing factor)

Splicing regulatory glutamine/lysine-rich protein 1 (Serine/arginine-rich-splicing Q8WXA9 SRE 1 regulatory protein 86) (SRrp86) (Splicing 508 FALSE FALSE FALSE FALSE FALSE FALSE factor, arginine/serine-rich 12) (Splicing regulatory protein 508) (SRrp508) Squalene monooxygenase (EC 1.14.14.17) Q14534 SQLE 574 FALSE FALSE FALSE FALSE TRUE FALSE (Squalene epoxidase) (SE)

Squalene synthase (SQS) (SS) (EC 2.5.1 .21) P37268 FDFT1 (FPP:FPP farnesyitransferase) (Farnesyl- 417 FALSE FALSE FALSE FALSE FALSE FALSE diphosphate farnesyitransferase)

Squamous cell carcinoma antigen recognized by T-ce!is 3 (SART-3) (Tat-interacting protein Q15020 SART3 963 FALSE FALSE FALSE FALSE FALSE FALSE of 11 kDa) (Tip1 10) (p1 10 nuclear RNA- binding protein) SRA stem-loop-interacting RNA-binding Q9GZT3 SL!RP 109 TRUE TRUE TRUE FALSE FALSE TRUE protein, mitochondrial SRSF protein kinase 1 (EC 2.7.1 1.1) (SFRS protein kinase 1) (Serine/arginine-rich protein- Q96SB4 SRPK1 655 TRUE FALSE TRUE TRUE FALSE FALSE specific kinase 1) (SR-protein-specific kinase 1) Staphylococcal nuclease domain-containing protein 1 (100 kDa coactivator) (EBNA2 Q7KZF4 SND1 910 FALSE FALSE FALSE FALSE FALSE FALSE coactivator p100) (Tudor domain-containing protein 11) (p100 co-activator) Staihmin (Leukemia-associated phosphoprotein ρ18) (Metablastin) STMN1 149 FALSE FALSE FALSE FALSE FALSE FALSE (Oncoprotein 18) (Op18) (Phosphoprotein p19) (pp19) (Prosolin) (Protein Pr22) (pp17)

Sterol-4-alpha-carboxylate 3-dehydrogenase, Q15738 NSDHL decarboxyiating (EC . . 1 .170) (Protein 373 TRUE TRUE TRUE FALSE TRUE TRUE H105e3) Stimulator of interferon genes protein (hST G) (Endoplasmic reticLflum interferon Q86WV6 TMEM173 stimulator) (ERiS) (Mediator of RF3 379 FALSE FALSE FALSE FALSE FALSE FALSE activation) (hMITA) (Transmembrane protein 173) Stomatin-like protein 2 , mitochondrial (SLP-2) Q9UJZ1 STOML2 (EPB72-like protein 2) (Paraproiein target 7) 356 FALSE FALSE FALSE TRUE TRUE TRUE (Paratarg-7)

Stress-70 protein, mitochondrial (75 kDa glucose-regulated protein) (GRP-75) (Heat Ρ38646 HSPA9 679 FALSE FALSE FALSE FALSE FALSE FALSE shock 70 kDa protein 9) (Mortaiin) (MOT) (Peptide-binding protein 74) (PBP74)

Stress-induced-phosphoprotein 1 (STM) (Hsc70/Hsp90-organizing protein) (Hop) P31948 STIP1 (Renal carcinoma antigen NY-REN-1 1) 543 FALSE FALSE FALSE FALSE FALSE FALSE (Transformation-sensitive protein lEF SSP 3521) Q13586 STIM1 Stromal interaction molecule 1 685 TRUE FALSE FALSE FALSE FALSE FALSE Structural maintenance of chromosomes A6NHR9 SMCHD1 flexible hinge domain-containing protein 1 2005 TRUE TRUE TRUE TRUE TRUE TRUE (SMC hinge domain-containing protein 1) Structural maintenance of chromosomes

Q14683 SMC1A protein 1A (SMC protein 1A) (SMC-1-alpha) 1233 TRUE TRUE TRUE F LS Ε F L Ξ F LS EE (SMC-1A) (Sb1 .8) Structural maintenance of chromosomes protein 2 (SMC protein 2) (SMC-2) 095347 SMC2 1197 FALSE FALSE FALSE FALSE FALSE FALSE (Chromosome-associated protein E) (hCAP-E) (XCAP-E homolog) Structural maintenance of chromosomes protein 3 (SMC protein 3) (SMC-3) (Basement membrane-associated chondroitin Q9UQE7 S C3 1217 FALSE FALSE FALSE FALSE FALSE FALSE proteoglycan) (Bamacan) (Chondroitin sulfate proteoglycan 6) (Chromosome-associated polypeptide) (hCAP) Structural maintenance of chromosomes protein 4 (SMC protein 4) (SMC-4) SMC4 1288 FALSE FALSE FALSE FALSE FALSE FALSE (Chromosome-associated polypeptide C) (hCAP-C) (XCAP-C homolog) Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 664 FALSE FALSE FALSE FALSE FALSE FALSE 1.3.5.1) (Flavoprotein subunit of complex ) (Fp) Succinate dehydrogenase [ubiquinone] iron- P21912 SDHB sulfur subunit, mitochondrial (EC 1.3.5.1) (iron- 280 FALSE FALSE FALSE TRUE TRUE TRUE sulfur subunit of complex II) (Ip) Succinate-CoA ligase [ADP-forrning] subunit beta, mitochondrial (EC 6.2.1 .5) (ATP-specific Q9P2R7 SUCLA2 succinyl-CoA synthetase subunit beta) (A- 463 FALSE TRUE FALSE FALSE FALSE FALSE SCS) (Succinyl-CoA synthetase beta-A chain) (SCS-betaA) Succinate-CoA ligase [ADP/GDP-forming] s a n a P53597 SUCLG1 'P >mitochondrial (EC 6.2.1 .4) (EC 346 FALSE FALSE FALSE FALSE FALSE FALSE 6.2.1 .5) (Succinyl-CoA synthetase subunit alpha) (SCS-alpha) Succinate-CoA ligase [GDP-forming] subunit beta, mitochondrial (EC 6 2.1.4) (GTP~specific Q96I99 SUCLG2 succinyl-CoA synthetase subunit beta) (G- 432 TRUE FALSE FALSE TRUE TRUE TRUE SCS) (GTPSCS) (Succinyl-CoA synthetase beta-G chain) (SCS-betaG) Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) (3- P558Q9 OXCT1 oxoac d CoA-transferase 1) (Somatic-type 520 FALSE FALSE FALSE FALSE FALSE FALSE succinyl-CoA:3-oxoacid CoA-transferase) (SCOT-s) SUMO-activating enzyme S fb u n t 1 (Ubiquitin- ike 1-activating enzyme E1A) [Cleaved into: Q9UBEQ SAE1 6 FALSE FALSE FALSE TRUE TRUE FALSE SUMO-activating enzyme subunit 1, N- terminally processed] SUMO-activating enzyme subunit 2 (EC 6.3.2.- ) (Anthracycline-associated resistance ARX) Q9UBT2 UBA2 640 FALSE FALSE FALSE TRUE TRUE FALSE (Ubiquitin-like 1-activafing enzyme E 1B) (Ubiquitin-like modifier-activating enzyme 2) SUMO-conjugating enzyme UBC9 (EC 2.3.2.-) (RING-type E3 SUMO transferase UBC9) (SUMO-protein ligase) (Ubiquitin carrier P63279 UBE2I 158 TRUE FALSE FALSE FALSE FALSE FALSE protein 9) (Ubiquitin carrier protein !) (Ubiquitin- conjugating enzyme E2 i) (Ubiquitin-protein ligase i) (p18) SUN domain-containing protein 1 (Protein unc- SUN1 812 FALSE FALSE FALSE FALSE FALSE FALSE 84 homoiog A) (Sad1/unc-84 protein-like 1) Superkiiler viraiicidic activity 2-like 2 (EC 3.6.4.13) (ATP-dependent RNA heiicase P42285 SKIV2L2 2 FALSE FALSE FALSE FALSE FALSE FALSE DOB1) (ATP-dependent RNA heiicase SKIV2L2) (TRAMP-like complex heiicase) Suppressor of SWI4 1 homolog (Ssf-1) (Brix Q9NQ55 PPAN domain-containing protein 3) (Peter Pan 3 FALSE FALSE FALSE FALSE FALSE FALSE homolog) Q6UWP8 SBSN Suprabasin 590 FALSE FALSE FALSE FALSE FALSE FALSE 015260 SURF4 Surfeit locus protein 4 269 FALSE FALSE FALSE FALSE FALSE FALSE SURP and G-patch domain-containing protein Q8IX01 SUGP2 2 (Arginine/serine-rich-splicing factor 14) 1082 FALSE FALSE FALSE FALSE FALSE TRUE (Splicing factor, arginine/serine-rich 14) Survival motor neuron protein (Component of Q16637 SMN1 294 FALSE FALSE FALSE FALSE FALSE FALSE gems 1) (Gemin-1)

SWI/SNF complex subunit SMARCC1 (BRG1- associated factor 155) (BAF155) (SWI/SNF Q92922 " complex 155 kDa subunit) (SWi/SNF-reiated 1105 TRUE FALSE FALSE TRUE TRUE TRUE matrix-associated actin-dependent regulator of chromatin subfamily C member 1)

SWI/SNF complex subunit SMARCC2 (BRG1- associated factor 170) (BAF170) (SWI/SNF S ARCC Q8TAQ2 complex 170 kDa subunit) (SWI/SNF-related 1214 TRUE TRUE FALSE FALSE TRUE TRUE matrix-associated actin-dependent regulator of chromatin subfamily C member 2)

SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily A SMARCA member 5 (SWI/SNF-related rnatrix- 060264 1052 FALSE FALSE FALSE FALSE FALSE FALSE 5 associated actin-dependent regulator of chromatin A5) (EC 3 6 4.-) (Sucrose nonfermenting protein 2 homolog) (hSNF2H)

SWi/SNF-reiated matrix-associated actin- S ARCB regulator of chromatin subfamily B member 1 (BRG1 -associated factor 47) 385 FALSE TRUE FALSE FALSE FALSE FALSE (BAF47) (integrase interactor 1 protein) (SNF£ homolog) (hSNF5) SWI/SNF-relaied matrix-associated actin- dependent regulator of chromatin subfamily D 1ARCD Q92925 member 2 (60 kDa BRG-1/Brm-associated 531 FALSE FALSE FALSE TRUE TRUE TRUE 2 factor subunit B) (BRG1 -associated factor 60B) (BAF60B) SWI/SNF-relaied matrix-associated actin- ARCE dependent regulator of chromatin subfamily E Q969G3 4 11 FALSE FALSE FALSE FALSE TRUE FALSE 1 member 1 (BRG1 -associated factor 57) (BAF57) Q92797 3Y PK Symplekin 1274 FALSE TRUE TRUE TRUE TRUE TRUE Synaptic vesicle membrane protein VAT-1 Q99536 VAT1 393 FALSE FALSE FALSE FALSE FALSE FALSE homolog (EC 1.-.-.-) 0 5498 YKT6 Synaptobrevin homolog YKT6 (EC 2.3.1.-) 198 FALSE FALSE FALSE FALSE FA L FALSE

Q 16563 Synaptophysin-like protein 1 (Pantophysin) 259 FALSE TRUE FALSE FALSE FALSE FALSE

Syntaxin-4 (Renal carcinoma antigen NY-REN Q 12846 297 F S ! F F L F LS FALSE FALSE 31) Syntaxin-binding protein 2 (Protein unc-18 STXBP2 homolog 2) (Unci 8-2) (Protein unc-18 593 FALSE FALSE FALSE FALSE FA LS FALSE homolog B) (Unc-18B) T-complex protein 1 subunit alpha (TCP-1 - P17987 TCP1 556 FALSE FALSE F L FA L FALSE FALSE alpha) (CCT-alpha) T-complex protein 1 subunit beta (TCP-1 - P78371 CCT2 535 FALSE FALSE FALSE FALSE FALSE FALSE beta) (CCT-beta) T-complex protein 1 subunit delta (TCP-1 - P50991 CCT4 delta) (CCT-deita) (Stimulator of TAR RNA- 539 FALSE FALSE FALSE FALSE FALSE FALSE binding) T-complex protein 1 subunit epsilon (TCP-1- P48643 CCT5 541 FALSE FALSE FALSE FALSE FALSE FALSE epsilon) (CCT-epsilon) T-complex protein 1 subunit eta (TCP-1 -eta) (CCT-eta) (HIV-1 Nef-interacting protein) Q99832 CCT7 543 FALSE FALSE FALSE FALSE FALSE FALSE [Cleaved into: T-complex protein 1 subunit eta, N-termina!ly processed] T-complex protein 1 subunit gamma (TCP-1 - P49368 CCT3 545 FALSE FALSE FALSE FALSE FALSE FALSE gamma) (CCT-gamma) (hTRiC5) T-complex protein 1 subunit theta (TCP-1- 550990 CCT8 theta) (CCT-theta) (Renal carcinoma antigen 548 FALSE FALSE FALSE FALSE FALSE FALSE NY-REN-15) T-complex protein 1 subunit zeta (TCP-1-zeta) P40227 CCT6A (Acute morphine dependence-related protein 531 FALSE FALSE FALSE FALSE FALSE FALSE 2) (CCT-zeta-1) (HTR3) (Tcp2Q)

Q9Y490 TLN1 Talin-1 2541 FALSE FALSE FALSE FALSE FALSE FALSE Q13148 TARDBP TAR DNA-binding protein 43 (TDP-43) 414 FALSE FALSE FALSE FALSE FALSE FALSE Q96GM8 TOE1 Target of EGR1 protein 1 510 FALSE FALSE FALSE FALSE FALSE FALSE Targeting protein forXklp2 (Differentially expressed in cancerous and non-cancerous lung ceils 2) (DIL-2) (Hepatocellular carcinoma- Q9ULW0 TPX2 associated antigen 519) (Hepatocellular 747 FALSE FALSE FALSE TRUE FALSE TRUE carcinoma-associated antigen 90) (Protein fls353) (Restricted expression proliferation- associated protein 100) (p100) TATA box-binding protein-like protein 1 (TBP- ike protein 1) (21 kDa TBP-like protein) (Second TBP of unique DNA protein) (STUD) P62380 TBPL1 186 TRUE FALSE FALSE FALSE FALSE FALSE (TATA box-binding protein-related factor 2) (TBP-related factor 2) (TBP-like factor) (TBP- reiated protein) TATA-binding protein-associated factor 2N (68 kDa TATA-binding protein-associated factor) TAF15 592 FALSE FALSE FALSE FALSE FALSE FALSE (TAF(li)68) (TAFII68) (RNA-binding protein 56) TBC1 domain family member 15 (GTPase- Q8TC07 TBC1D15 activating protein RAB7) (GAP for RAB7) 691 TRUE FALSE FALSE TRUE TRUE TRUE (Rab7-GAP) TEL02-interacting protein 1 homolog (Protein 043156 TTM 1089 TRUE FALSE FALSE FALSE FALSE FALSE S G10) Telomeric repeat-binding factor 2-interacting protein 1 (TERF2~interacting telomeric protein 1) (TRF2-interacting telomeric protein 1) Q9NYB0 TERF2IP 399 FALSE FALSE FALSE FALSE FALSE FALSE (Dopamine receptor-interacting protein 5) (Repressor/activator protein 1 bomoiog) (RAP1 homoiog) (hRap1) Tetratricopeptide repeat protein 1 (TPR repeat Q99614 TTC1 FALSE FALSE FALSE FALSE FALSE FALSE protein 1) Tetratricopeptide repeat protein 4 (TPR repeat 095801 TTC4 TRUE TRUE TRUE FALSE FALSE FALSE protein 4)

TFI!H basal transcription factor complex helicase XPB subunit (EC 3.6.4 12) (Basic transcription factor 2 89 kDa subunit) (BTF2 p89) (DNA excision repair protein ERCC-3) P19447 (DNA repair protein complementing XP-B 782 TRUE TRUE TRUE FALSE FALSE FALSE ceils) (TFI!H basal transcription factor complex 89 kDa subunit) (TF H 89 kDa subunit) (TF!IH •J\ p89) (Xeroderma pigmentosum group B- complementing protein)

Thi t oligopeptidase (EC 3.4.24.15) P52888 THOP1 689 FALSE FALSE FALSE FALSE TRUE FALSE (Endopeptidase 24.15) (MP78)

Thioredoxin domain-containing protein 17 (14 Q9BRA2 TXNDC17 kDa tbioredoxin-relafed protein) (TRP14) 12 3 F . 3 E F S F . 3 E FALSE FALSE FALSE (Protein 42-9-9) (Thioredoxin-like protein 5) Thioredoxin domain-containing protein 5 (Endoplasmic reticulum resident protein 48) Q8NBS9 TXNDC5 432 FALSE FALSE FALSE FALSE FALSE FALSE (ER protein 46) (ERp46) (Thioredoxin-like protein p46) Thioredoxin (Trx) (ATL-derived factor) (ADF) P10599 TXN (Surface-associated sulphydryl protein) 105 FALSE FALSE FALSE FALSE FALSE FALSE (SASP) Thioredoxin reductase , cytoplasmic (TR) (EC 1.8.1 .9) (Gene associated with retinoic and inierferon-induced mortality 12 protein) TXNRD1 (GRIM-12) (Gene associated with retinoic and 649 TRUE FALSE FALSE TRUE TRUE FALSE IFN-induced mortality 12 protein) (KM-102- derived reductase-like factor) (Thioredoxin reductase TR1) Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1. 1 1. 1 .15) (Antioxidant PRDX3 protein 1) (AOP-1) (HBC189) (Peroxiredoxin 256 TRUE FALSE FALSE TRUE TRUE TRUE III) (Prx-lll) (Peroxiredoxin-3) (Protein ER5 homolog) Thioredoxin-like protein 1 (32 kDa fhioredoxin- Q43396 TXNL1 289 FALSE FALSE FALSE FALSE FALSE FALSE related protein)

Thioredoxin-related transmembrane protein 1

Q9H3N1 T X 1 (Thioredoxin domain-containing protein 1) 280 TRUE TRUE FALSE F LS Ε F L Ξ F 3 EE (Transmembrane Trx-related protein)

Thioredoxin-related transmembrane protein 2 Q9Y320 T X2 (Cell proliferation-inducing gene 26 protein) 296 FALSE TRUE FALSE FALSE TRUE FALSE (Thioredoxin domain-containing protein 14)

Q8NI27 THOC2 THO complex subunit 2 (Tho2) (hTREX120) 1593 FALSE FA S E FA 3 E FALSE FALSE FALSE

THO complex subunit 3 (Tho3) (TEX1 Q96J01 THOC3 351 FALSE FALSE FA 3 E TRUE FALSE TRUE homolog) (hTREX45) THO complex subunit 4 (Tho4) (Ally of AML-1 and LEF-1) (Aly/REF export factor) Q86V81 ALYREF 257 FALSE FALSE FALSE FALSE FALSE FALSE (Transcriptional coactivator Aly/REF) (bZIP- enhancing factor BEF)

THO complex subunit 5 homolog (Functional spliceosome-associated protein 79) (fSAP79) Q 13769 THOC5 683 TRUE FALSE FALSE TRUE TRUE FALSE (NF2/meningioma region protein pK1 .3) (Placental protein 39.2) (PP39.2) (hTREX90) THO complex subunit 6 homoiog (Functional Q86W42 spliceosome-associaied protein 35} (fSAP35) 341 FALSE FALSE FALSE FALSE FALSE FALSE (WD repeat-containing protein 58)

Threonine-tRNA ligase, cytoplasmic (EC P26639 TARS 723 FALSE FALSE FALSE FALSE FALSE FALSE 6.1 . 1 .3) (Threonyi-tRNA synthetase) (ThrRS)

Threonylcarbamoyladenosine tRNA methylthiotransferase (EC 2.8.4.5) (CDK5 Q5VV42 CDKAL1 579 FALSE TRUE FALSE FALSE TRUE FALSE regulatory subunit-associated protein 1-like 1) (tRNA-t(6)A37 methylthiotransferase) THU PD Q9NXG2 THUMP domain-containing protein 1 353 FALSE! FALSEi FALSE FALSE FALSE FALSE 1 Thymidylate kinase (EC 2.7.4.9) (dT P P23919 DTY K 212 FALSE! FALSE FALSE FALSE FALSE FALSE kinase) Thymidylate synthase (TS) (TSase) (EC P04818 TY S 3 3 FALSE FALSE FALSE FALSE FALSE FALSE 2.1 . 1 .45) Thyroid hormone receptor-associated protein 3 (Thyroid hormone receptor-associated Q9Y2W1 THRAP3 955 FALSE FALSE FALSE FALSE FALSE FALSE protein complex 150 kDa component) (Trap150) TIP41-iike protein (Putative MAPK-activating 075663 TIPRL protein PM10) (Type 2A-interacting protein) 272 FALSE FALSE FALSE FALSE FALSE FALSE (TIP)

Titin (EC 2 7.11.1) (Connectin) Q8WZ42 TTN 34350 FALSE FALSE FALSE FALSE FALSE FALSE (Rhabdomyosarcoma antigen MU- S-40.14) TOR1AIP Torsin-1A-interacting protein 1 (Lamin- Q5JTV8 583 FALSE FALSE FALSE FALSE FALSE FALSE 1 associated protein 1B) (LAP1 B)

TP53-regulating kinase (EC 2 7.11.1) (Atypical serine/threonine protein kinase TP53RK) Q96S44 TP53RK 253 FALSE FALSE FALSE FALSE FALSE FALSE (EKC/KEOPS complex subunit TP53RK) (EC 3.6.-.-) (Nori-2) (p53-related protein kinase)

P37837 TALDQ1 Transaldoiase (EC 2.2.1 .2) 337 FALSE FALSE FALSE FALSE FALSE FALSE Transcription activator BRG1 (EC 3.6.4.-) (ATP-dependent heiicase SMARCA4) (BRG1- associated factor 190A) (BAF190A) (Mitotic SMARCA growth and transcription activator) (Protein 1647 FALSE FALSE FALSE FALSE FALSE FALSE 4 BRG-1) (Protein brahma homolog 1) (SNF2- beta) (SW /SNF re a ed matrix-associated actin-dependent regulator of chromatin subfamily A member 4)

Transcription elongation factor A protein 1 P23193 TCEA1 (Transcription elongation factor S-i protein 1) 301 FALSE FALSE FALSE FALSE FALSE FALSE (Transcription elongation factor TFNS.o) Elongin-C (EloC) (Elongin 5 kDa subunit) (RNA polymerase transcription factor SMI Q15369 ELOC 112 TRUE FALSE FALSE FALSE FALSE FALSE subunit C) (SHI p15) (Transcription elongation factor B polypeptide 1) Elongin-B (EioB) (Elongin 18 kDa subunit) (RNA polymerase II transcription factor S I Q15370 ELOB 118 FALSE FALSE FALSE FALSE TRUE FALSE subunit B) (Sill p18) (Transcription elongation factor B polypeptide 2)

Transcription elongation factor SPT5 (hSPT5) (DRB sensitivity-inducing factor 1 0 kDa SUPT5H subunit) (DSIF p160) (DRB sensitivity-inducing 1087 FALSE FALSE FALSE FALSE FALSE FALSE factor large subunit) (DSIF large subunit) (Tat- cotransactivator 1 protein) (Tat-CT1 protein)

Transcription elongation regulator 1 (TATA O14776 TCERG1 box-binding protein-associated facior 2S) 1098 FALSE TRUE FALSE FALSE FALSE FALSE (Transcription factor CA1 50) Transcription factor A , mitochondrial (mtTFA) (Mitochondrial transcription factor 1) (MtTF1) Q00059 246 FALSE FALSE FALSE FALSE TRUE FALSE (Transcription factor 6) (TCF-6) (Transcription facior 6-like 2) Transcription factor BTF3 (Nascent polypeptide-associated complex subunit beta) P20290 BTF3 206 FALSE FALSE FALSE FALSE FALSE FALSE (NAC-beta) (RNA polymerase B transcription factor 3)

Transcription factor p65 (Nuclear factor NF- RELA kappa-B p65 subunit) (Nuclear factor of kappa 551 TRUE FALSE FALSE FALSE FALSE TRUE light polypeptide gene enhancer in B-ce s 3)

Transcription initiation factor HE subunit beta P29084 GTF2E2 (TFIIE-beta) (General transcription factor E 291 FALSE FALSE FALSE FALSE FALSE FALSE subunit 2) Transcription initiation factor TFIID subunit 10 (STAF28) (Transcripiion initiation factor TFIID Q12962 TAF10 218 FALSE FALSE! FALSE FALSE FA LS 30 kDa subunit) (TAF(II)30) (TAFii-30) (TAFII30) Transcription intermediary factor 1-beta (TIF1- beta) (E3 SUMO-protein ligase TRIM28) (EC 2.3.2.27) (KRAB-associated protein 1) (KAP- 1) (KRAB-interacting protein 1) (KRIP-1) Q13263 TRI 28 835 FALSE FALSE L FALSE FALSE FALSE (Nuclear corepressor KAP-1) (RING finger protein 96) (RING-type E3 ubiquitin transferase T F1-beta) (Tripartite motif- containing protein 28) Transcriptional activator protein Pur-alpha Q00577 PURA (Purine-rich single-stranded DNA-binding 322 FALSE FALSE FALSE TRUE FALSE FALSE protein alpha) Transcriptional repressor CTCF ( 1 1-zinc finger P4971 1 CTCF protein) (CCCTC-binding factor) (CTCFL 727 FALSE FALSE FALSE FALSE FALSE FALSE paralog) GATAD2 P repressor p66-alpha Q86YP4 (Hp66alpha) (GATA zinc finger domain- 633 TRUE FALSE TRUE TRUE FALSE FALSE A containing protein 2A) Transcriptional repressor p66-beta (GATA GATAD2 Q8WXI9 ' " zinc finger domain-containing protein 2B) 593 FALSE FALSEi FALSE! FALSE FALSE FALSE (p66/p68) Transducin beta-like protein 2 ( S beta- transducin repeats protein) (WS-betaTRP) Q9Y4P3 TBL2 447 FALSE FALSE FALSE FALSE TRUE TRUE (Williams-Beuren syndrome chromosomal region 13 protein) Transducin beta-like protein 3 (WD repeat- Q 12788 TBL3 808 FALSE FALSE FALSE FALSE FALSE FALSE containing protein SAZD) Transferrin receptor protein 1 (TR) (TfR) (TfR1 ) (Trfr) (T9) (p90) (CD antigen CD71 ) Ρ 02786 TFRC 760 FALSE FALSE FALSE FALSE FALSE FALSE [Cleaved into: Transferrin receptor protein 1, serum form (sTfR)] Transformer-2 protein homolog alpha (TRA-2 Q 3595 TRA2A alpha) (TRA2-alpha) (Transformer-2 protein 282 FALSE FALSE FALSE F 3 E F FALSE homolog A) Transformer-2 protein homolog beta (TRA-2 beta) (TRA2-beta) (hTRA2-beta) (Splicing Ρ 62995 TRA2B 288 FALSE F FALSE factor, arginine/serine-rich 10) (Transformer-2

FALSE

Transgelin-2 (Epididymis tissue protein Li 7e) Ρ 37802 TAGLN2 199 FALSE F FALSE (SM22-aipha homolog) Transitional endoplasmic reticulum ATPase (TER ATPase) (EC 3.6 4.6) ( 15S g(2 )~ Ρ 55072 VCP 806 FALSE FALSE FALSE FALSE FALSE FALSE ATPase p97 subunit) (Valosin-containing protein) (VCP) Ρ 29401 τκτ Transketoiase (TK) (EC 2.2. 1 1) 623 FALSE FALSE FALSE FALSE FALSE FALSE Translation initiation factor elF-2B subunit Q9UI 10 E F2B4 delta (el F-2B GDP-GTP exchange factor 523 FALSE FALSE FALSE FALSE FALSE FALSE subunit delta) Translation initiation factor elF-2B subunit Q9NR50 E F2B3 gamma (e F-2B GDP-GTP exchange factor 452 FALSE FALSE FALSE FALSE FALSE FALSE subunit gamma)

Q96EY4 Translation machinery-associated protein 16 203 FALSE FALSE FALSE F F FALSE Translaiional!y-controlled tumor protein P 3693 TPT1 (TCTP) (Forti!in) (Histamine-releasing factor) 172 FALSE FALSE FALSE FALSE TRUE FALSE (HRF) (p23) Translin (EC 3 .1.-.-) (Component 3 of Q 5631 TSN 228 TRUE FALSE FALSE FALSE FALSE FALSE promoter of RISC) (C3PO) Translin-associated protein X (Translin- Q99598 TS AX 290 FALSE FALSE FALSE TRU E FALSE TRUE associated factor X) Translocating chain-associated membrane Q 5629 T RA 1 374 FALSE FALSE FALSE TRU E TRUE TRUE protein 1 Translocation protein SEC62 (Translocation Q99442 SEC62 399 FALSE FALSE FALSE TRU E FALSE FALSE protein 1) (TP-1 ) (hTP-1 ) Q9UGP8 SEC63 Translocation protein SEC63 homoiog 760 FALSE FALSE FALSE TRU E TRUE TRUE Transiocon-associated protein subunit delta P51 571 SSR4 (TRAP-deita) (Signal sequence receptor 173 TRUE TRUE FALSE TRUE TRUE TRUE subunit delta) (SSR-delta)

Transiocon-associated protein subunit gamma

Q9UNL2 SSR3 (TRAP-gamma) (Signal sequence receptor 185 F L3 Ε FA L Ξ F L3 Ε F 3 F 3 E FA 3 subunit gamma) (SSR-gamma)

Transmembrane 9 superfamily member 2 Q99805 T 9SF2 663 FALSE FALSE TRUE TRUE TRUE FALSE (p76) Transmembrane 9 superfamily member 3 Q9HD45 T 9SF3 589 FA 3 E FALSEL FA 3 E TRU E FALSE FALSE (EP70-P-iso) (SM-1 1044-binding protein) Transmembrane 9 superfamily member 4 Q92544 T 9SF4 642 FA 3 E FAL 3 E FA 3 E FALSE FALSE FALSE (Tumor cannibalism associated protein 1) Calcium load-activated calcium channel (CLAC channel) (Transmembrane and coiled- coi domain-containing protein 1) Q9UM00 T C0 1 FALSE TRUE FALSE FALSE TRUE FALSE (Transmembrane and coiled-coil domains protein 4) (Xenogeneic cross-immune protein PCIA3) Transmembrane and ubiquifin-like domain- containing proiein 1 (Dendritic cell-derived Q9BVT8 TMUB1 ubiquitin-like protein) (DULP) (Hepatocyte odd 246 FALSE FALSE FALSE FALSE FALSE FALSE protein shuttling protein) (Ubiquitin-like protein SB1 44) [Cleaved into: iHOPS] Transmembrane e p24 domain-containing protein 0 (21 kDa transmembrane-trafficking P49755 TMED10 protein) (S31III125) (S31 I125) (Tmp-21-l) 219 TRUE TRUE FALSE FALSE TRUE TRUE (Transmembrane protein Tmp21) (p23) (p24 family protein de!ta-1) (p24delta1) (p24delta)

Transmembrane emp24 domain-containing protein 4 (Endoplasmic reticulum stress- Q7Z7H5 T ED4 response protein 25) (ERS25) (GMP25iso) 227 FALSE FALSE FALSE TRUE TRUE FALSE (Putative NF-kappa-B-activating protein 156) (p24 family protein aipha-3) (p24aipha3)

Transmembrane emp24 domain-containing Q9Y3B3 T ED7 protein 7 (p24 family protein gamma-3) 224 FALSE FALSE FALSE FALSE FALSE FALSE (p24gamma3) (p27)

Transmembrane emp24 domain-containing Q9BVK6 T ED9 protein 9 (GIV3P25) (Glycoprotein 25L2) (p24 235 FALSE FALSE FALSE FALSE FALSE FALSE family protein aipha~2) (p24alpha2) (p25)

Transmembrane protein 109 (Mitsugumin-23) Q9BVC6 T l 1109 243 TRUE TRUE FALSE FALSE FALSE FALSE ( g23) 1126 Q9H061 Transmembrane protein 126A 195 FALSE FALSE FALSE FALSE FALSE FALSE A Transmembrane protein 165 (Transmembrane Q9HC07 TMEM165 protein PT27) (Transmembrane protein 324 FALSE FALSE FALSE FALSE FALSE FALSE TPARL)

Q6UW68 TMEM205 Transmembrane protein 205 189 FALSE FALSE FALSE TRUE FALSE FALSE

Q96SK2 TMEM209 Transmembrane protein 209 561 FALSE FALSE FALSE FALSE FALSE FALSE

Q9H330 TME 245 Transmembrane protein 245 (Protein CG-2) 9 11 FALSE FALSE FALSE FALSE FALSE FALSE

Transmembrane protein 33 (Protein DB83) P57088 T E 33 247 FALSE TRUE FALSE FALSE FALSE FALSE (SHINC-3) T E 41 Q5BJD5 Transmembrane protein 4 B 291 FALSE FALSE FALSE FALSE FALSE FALSE

Transportin-1 (Importin beta-2) (Karyopherin Q92973 TNP01 898 FALSE FALSE FALSE TRUE TRUE TRUE beta-2) (M9 region interaction protein) (MIP) 0 14787 TNP02 Transportin-2 (Karyopherin beta-2b) 897 FALSE FALSE TRUE FALSE FALSE FALSE Transportin-3 (lmportin-12) (Imp12) Q9Y5L0 TNP03 923 TRUE FALSE FALSE FALSE FALSE FALSE (Transportin-SR) (TRN-SR) Treacle protein (Treacher Collins syndrome Q13428 TCOF1 1488 FALSE FALSE FALSE FALSE FALSE TRUE protein) Tricarboxylate transport protein, mitochondrial (Citrate transport protein) (CTP) (Solute P53007 SLC25A1 3 11 FALSE FALSE FALSE FALSE FALSE FALSE carrier family 25 member 1) (Tricarboxylate carrier protein) Trifunctional enzyme subunit alpha, mitochondrial (78 kDa gastrin-binding protein) (TP-alpha) [Includes: Long-chain enoyl-CoA P40939 HADHA 763 TRUE TRUE TRUE F LS Ε F L Ξ F LS EE hydratase (EC 4.2 1.17); Long chain 3- 4- hydroxyacyl-CoA dehydrogenase (EC 1. 1 . 1 .21 1)] Trifunctional enzyme subunit beta, mitochondrial (TP-beta) [Includes: 3-ketoacyl- P55084 HADHB 474 TRUE TRUE FALSE TRUE TRUE FALSE CoA thioiase (EC 2.3.1 .16) (Acety!-CoA acyltransferase) (Beta-ketothiolase)] Trifunctional purine biosyniheiic protein adenosine-3 [includes: Phospboribosylarnine-- g!ycine iigase EC 6.3.4.13) (Giycinamide ribonucleotide synthetase) (GARS) (Phosphoribosylgiycinamide synthetase): Phosphoribosyiformylglycinamidine cy o- P22102 GART 1010 FALSE FALSE FALSE FALSE FALSE FALSE ligase (EC 6.3.3.1) (AIR synthase) (AIRS) (Phosphoribosyl-aminoimidazole synthetase); Phosphoribosylgiycinamide formyltransferase (EC 2.1 .2.2) (5'-phosphoribosylglycinamide transformy!ase) (GAR transformylase) (GART)]

Trimeric intracellular cation channel type B T E 38 Q9NW0 (TR!C-B) (TR!CB) (Transmembrane protein 291 FALSE FALSE FALSE FALSE FALSE FALSE 38B) Triosephosphate isomerase (TIM) (EC 4- P60 / 4 TPI1 286 FALSE FALSE FALSE FALSE FALSE FALSE 4- 5.3.1 .1) (Triose-phosphate isomerase) Tripeptidyl-peptidase 2 (TPP-2) (EC P29144 TPP2 3.4.14.10) (Tripeptidyl aminopeptidase) 1249 FALSE FALSE FALSE FALSE FALSE FALSE (Tripeptidyl-peptidase I ) (TPP-II) Q7Z2T5 TR T1L TRMT1-like protein (EC 2.1 . 1 .-) 733 FALSE FALSE FALSE FALSE FALSE FALSE tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TR T61A (EC 2.1 . 1 .220) Q96FX7 TR T61A (tRNA(m1A58)-methyltransferase subunit 289 FALSE FALSE FALSE FALSE FALSE FALSE TRMT61A) (tRNA(m1A58)MTase subunit TRMT6 )

tRNA (cytosine(34)-C(5))-methyltransferase (EC 2.1 . 1 .203) (Myc-induced SUN domain- containing protein) ( isu) (NOL1/NOP2/Sun Q08J23 NSUN2 domain family member 2) (Substrate of 767 FALSE FALSE FALSE FALSE FALSE FALSE A M /Aurora kinase B) (tRNA (cytosine-5-)- methyltransferase) (tRNA methyliransferase 4 homolog) (hTrrrs4) tRNA pseudouridine synihase A , mitochondrial (EC 5.4 99.12) (tRNA pseudouridine(38-40) Q9Y606 PUS1 427 TRUE TRUE FALSE FALSE FALSE TRUE synthase) (tRNA pseudouridylate synthase ) (tRNA-uridine isomerase ) tRNA-dihydrouridine(47) synthase [NAD(P)(+)]- Q96G46 DUS3L like (EC 1.3.1 .-) (tRNA-dihydrouridine 650 FALSE FALSE FALSE FALSE FALSE FALSE synthase 3-like) tRNA-splicing iigase RtcB homolog (EC Q9Y3IQ RTCB 5 5 FALSE FALSE FALSE FALSE FALSE FALSE 6.5.1 .3) Tropomodulin-3 (Ubiquitous tropomodulin) (U- Q9NYL9 T OD3 352 FALSE FALSE FALSE FALSE FALSE FALSE Tmod) Tropomyosin alpha-3 chain (Gamma- Ρ06753 TP 3 tropomyosin) (Tropomyosin-3) (Tropomyosin- 285 TRUE FALSE FALSE TRUE TRUE FALSE 5) (hTM5) Tropomyosin alpha-4 chain (TM30p1) Ρ67936 TP 4 248 FALSE FALSE FALSE FALSE FA LSE FALSE (Tropomyosin-4) Tryptophan-tRNA Iigase, cytoplasmic (EC 4- •J\ 6.1 . 1 .2) (Interferon-induced protein 53) Ρ23381 WARS (IFP53) (Tryptophanyl-tRNA synthetase) 471 FALSE FALSE FALSE FALSE FALSE FALSE (TrpRS) (hWRS) [Cleaved into: T1-TrpRS; T2- TrpRS] Tubulin aipha-1A chain (Alpha-tubulin 3) (Tubulin B-alpha-1) (Tubulin alpha-3 chain) Q71U36 TUBA1A 451 FALSE FALSE FALSE FALSE FALSE FALSE [Cleaved into: Detyrosinated tubulin alpha-1A chain] Tubulin alpha-1C chain (Alpha-tubulin 6) Q9BQE3 TUBA1C (Tubulin alpha-6 chain) [Cleaved into: 449 FALSE FALSE FALSE FALSE FALSE FALSE Detyrosinated tubulin aipha-1C chain] Tubulin aipha-4A chain (Alpha-tubulin 1) P68366 TUBA4A (Testis-specific alpha-tubulin) (Tubulin H2- 448 FALSE FALSE FALSE FALSE FALSE FALSE alpha) (Tubulin aipha-1 chain) P07437 TUBB Tubulin beta chain (Tubulin beta-5 chain) FALSE FALSE FALSE FALSE FALSE FALSE Tubulin beta-4B chain (Tubulin beta-2 chain) P68371 TUBB4B 445 FALSE FALSE FALSE FALSE FALSE FALSE (Tubulin beta-2C chain) Q9BUF5 TUBB6 Tubulin beta~6 chain (Tubulin beta class V) 446 FALSE FALSE FALSE FALSE FALSE FALSE

Q14166 TTLL12 Tubulin-tyrosine ligase-like protein 12 644 FALSE FALSE FALSE TRUE FALSE TRUE Tubulin-folding cofactor B (Cytoskeleton- associated protein 1) (Cytoskeleton- TBCB 244 TRUE FALSE FALSE FALSE FALSE FALSE associated protein CKAPI) (Tubulin-specific chaperone B) Tubulin-specific chaperone A (TCP1- 075347 TBCA chaperonin cofactor A) (Tubulin-folding 108 FALSE FALSE FALSE TRUE FALSE TRUE cofactor A) (CFA) Tubulin-specific chaperone D (Beta-tubulin Q9BTW9 TBCD cofactor D) (tfcD) (SSD-1) (Tubulin-folding 1192 TRUE FALSE FALSE TRUE TRUE TRUE cofactor D) Tubulin-specific chaperone E (Tubulin-folding Q15813 TBCE 2 FALSE! F LS E F L FALSE TRUE FA LS cofactor E) Tumor necrosis factor alpha-induced protein 8 (TNF alpha-induced protein 8) (Head and _ _, - , . „_ , . neck tumor and metastasis-related protein) » 198 FALSE FALSE A LSE FALSE FALSE FALSE (MDC-3.13) (NF-kappa-B-inducible DED- containing protein) (NDED) (SCC-S2) (T F- induced protein GG2-1) Tumor protein D54 (hD54) (Tumor protein D52 Q43399 TPD52L2 206 FALSE FALSE FALSE TRUE FALSE FALSE like 2) TP53-binding protein 1 (53BP1) (p53-binding Q12888 TP53BP1 1972 FALSE FALSE TRUE FALSE FALSE FALSE protein 1) (p53BP1) Tumor susceptibility gene 101 protein (ESCRT Q99816 TSG101 390 FALSE FALSE FALSE FALSE FALSE FALSE complex subunit TSG101) Twinfilin-2 (A8-related protein) (hA6RP) Q6IBS0 TWF2 (Protein tyrosine kinase 9-like) (Twinfilin-1-like 349 FALSE FALSE FALSE TRUE TRUE TRUE protein)

Tyrosine-tRNA ligase, cytoplasmic (EC 6.1 . 1 .1) (Tyrosyl-tRNA synthetase) (TyrRS) P54577 YARS 528 FALSE FALSE FALSE FALSE FALSE FALSE [Cleaved into: Tyrosine-tRNA ligase, cytoplasmic, N-terminally processed] Tyrosine-proiein kinase ΒΑΖ Β (EC 2.7.10.2) (Bromodomain adjacent to zinc finger domain protein 1B) (Williams syndrome transcription Q9UIG0 ΒΑΖ Β factor) (Williams-Beuren syndrome 1483 TRUE TRUE TRUE TRUE TRUE TRUE chromosomal region 1 protein) (Williams- Beuren syndrome chromosomal region 9 protein) (hWALp2)

Tyrosine-protein kinase CSK (EC 2 7.10.2) (C- CSK 450 FALSE TRUE FALSE FALSE FALSE FALSE Src kinase) (Protein-tyrosine kinase CYL) Tyrosine-protein phosphatase non-receptor Ρ18031 ΡΤΡΝ 1 type 1 (EC 3.1 .3.48) (Protein-tyrosine 435 FALSE FALSE FALSE TRUE TRUE TRUE phosphatase 1B) (PTP-1 B) U 1 small nuclear ribonudeoprotein 70 kDa Ρ08621 SNRNP70 437 FALSE FALSE FALSE FALSE FALSE FALSE (U1 snRNP 70 kDa) (U1-70K) (snRNP70) U 1 small nuclear ribonudeoprotein C (U1 Ρ09234 SNRPC 159 FALSE FALSE FALSE FALSE TRUE TRUE snRNP C) (U1-C) (U1C) U2 small nuclear ribonudeoprotein A' (U2 4- Ρ09661 SNRPA1 2 F L3 Ε FA L Ξ F L3 Ε F LS Ε FAL Ξ FAL3 EE -4 snRNP A') U2 small nuclear ribonudeoprotein B" (U2 Ρ08579 SNRPB2 225 FAL3 Ε FA 3 Ξ FAL3 FA 3 FA 3 EE FAL3 EE snRNP B")

U2 snRNP-associated SURP motif-containing 015042 U2SURP protein (140 kDa Ser/Arg-rich domain protein) 1029 FALSE FALSE FALSE FALSE FALSE TRUE (U2-associated protein SR140)

U3 small nucleolar ribonudeoprotein protein Q9NV31 1P3 184 FALSE FALSE FALSE FALSE FALSE FALSE IMP3 (U3 snoRNP protein IMP3) (BRMS2)

1PHOSP U3 small nucleolar ribonudeoprotein protein 000566 681 FALSE FALSE FALSE TRUE FALSE FALSE H10 PP10 (M phase phosphoprotein 10)

U3 small nucleolar RNA-associated protein 15 Q8TED0 UTP15 518 TRUE FALSE FALSE FALSE FALSE TRUE homo!og

U3 small nucleolar RNA-associated protein 18 Q9Y5J1 UTP18 556 FALSE FALSE FALSE FALSE FALSE FALSE homolog (WD repeat-containing protein 50) U3 small nucleolar RNA-associaied protein 4 Q969X6 UTP4 homo!og (Cirhin) (UTP4 small subunit 386 TRUE TRUE TRUE FALSE FALSE FALSE processome component) U3 small nucleolar RNA-associated protein 6 homo!og (Hepatocellular carcinoma- G9NYH9 UTP6 597 FALSE TRUE TRUE FALSE TRUE TRUE associated antigen 66) (Multiple hat domains protein) U3 small nucleolar RNA-interacting protein 2 (RRP9 homolog) (U3 small nucleolar 043818 RRP9 ribonucleoprotein-associated 55 kDa protein) 475 FALSE FALSE FALSE TRUE TRUE TRUE (U3 snoRNP-associated 55 kDa protein) (U3- 55K) U4/U6 small nuclear ribonucleoprotein Prp3 043395 PRPF3 (Pre-mRNA-splicing factor 3) (hPrp3) (U4/U6 683 TRUE FALSE FALSE FALSE FALSE FALSE snRNP 90 kDa protein) U4/U6 small nuclear ribonucleoprotein Prp31 (Pre-mRNA-processing factor 31) Q8WWY3 PRPF31 (Serologically defined breast cancer antigen 499 FALSE FALSE FALSE FALSE FALSE FALSE NY-BR-99) (U4/U6 snRNP 6 1 kDa protein) (Protein 6 1K) (hPrp31) U4/U6 small nuclear ribonucleoprotein Prp4 043172 PRPF4 (PRP4 homolog) (hPrp4) (U4/U6 snRNP 60 522 FALSE FALSE FALSE FALSE FALSE FALSE kDa protein) (WD splicing factor Prp4) U4/U6.U5 tri-snRNP-associated protein 1 (SNU66 homolog) (hSnu66) (Squamous cell carcinoma antigen recognized by T-celis 1) 043290 SART1 800 TRUE FALSE FALSE TRUE TRUE FALSE (SART-1) (hSART-1) (U4/U6.U5 tri-snRNP- associated 110 kDa protein) (allergen Horn s 1) U4/U6.U5 tri-snRNP-associated protein 2 (inactive ubiquitin-specific peptidase 39) Q53GS9 USP39 565 FALSE FALSE FALSE FALSE FALSE FALSE (SAD1 homolog) (U4/U6.U5 tri-snRNP- associated 65 kDa protein) (65K) U5 small nuclear ribonudeoproiein 200 kDa helicase (EC 3.6.4.13) (Activating signal cointegrator 1 complex subunit 3- ke 1) 2136 FALSE FALSE FALSE FALSE FALSE FALSE (BRR2 homolog) (U5 snRNP-specific 200 kDa protein) (U5-200KD)

U5 small nuclear ribonucieoprotein 40 kDa protein (U5 snRNP 40 kDa protein) (U5-40K) SNRNP40 (38 kDa-splicing factor) (Prp8-binding protein) 357 TRUE TRUE TRUE TRUE TRUE TRUE (hPRPSBP) (U5 snRNP-specific 40 kDa protein) (WD repeat-containing protein 57)

U6 snRNA-associated Sm-like protein LSm2 (Protein G7b) (Small nuclear ribonuclear Q9Y333 LS 2 95 FALSE FALSE! FALSE FALSE FA LS protein D homolog) (snRNP core Sm-like protein Sm-x5) Ubiquilin-1 (Protein linking !AP with Q9U X0 UBQLN1 589 TRUE F LS E FALSE! FALSE TRUE TRUE cytoskeleton 1) (PLIC-1) (hPLIC-1)

4- Ubiquilin-2 (Chapl) (DSK2 homolog) (Protein UBQLN2 linking !AP with cytoskeleton 2) (PLiC-2) 624 FALSE FALSE A LSE FALSE FALSE FALSE (hPL!C~2) (Ubiquitin-like product Chap1/Dsk2)

Ubiquitin carboxyl-terminai hydrolase 10 (EC 3.4.19.12) (Deubiquitinating enzyme 10) Q14694 USP10 798 FALSE FALSE FALSE FALSE FALSE FALSE (Ubiquitin thioesterase 10) (Ubiquitin-specific- processing protease 10) Ubiquitin carboxyl-terminai hydrolase 14 (EC 3.4.19.12) (Deubiquitinating enzyme 14) P54578 USP14 494 FALSE FALSE FALSE FALSE FALSE FALSE (Ubiquitin thioesterase 1 ) (Ubiquitin-specific- processing protease 14) Ubiquitin carboxyl-terminai hydrolase 19 (EC 3.4.19.12) (Deubiquitinating enzyme 19) 094966 USP19 (Ubiquitin thioesterase 19) (Ubiquitin-specific- 1318 FALSE FALSE FALSE FALSE FALSE FALSE processing protease 19) (Zinc finger YND domain-containing protein 9) Ubiquitin carboxyl-terminai hydrolase 24 (EC 3.4. 9 12) (Deubiquitinating enzyme 24) Q9UPU5 USP24 2620 FALSE FALSE FALSE FALSE FALSE FALSE (Ubiquitin thioesterase 24) (Ubiquitin-specific- processing protease 24)

Ubiquitin carboxyl-terminai hydrolase 5 (EC 3.4.19.12) (Deubiquitinating enzyme 5) P45974 USPS 858 FALSE FALSE FALSE FALSE FALSE FALSE (Isopeptidase T) (Ubiquitin thioesterase 5) (Ubiquitin-specific-processing protease 5)

Ubiquitin carboxyl-terminai hydrolase 7 (EC 3.4.19.12) (Deubiquitinating enzyme 7) Q93009 USP7 (Herpesvirus-associated ubiquitin-specific 1102 FALSE FALSE FALSE FALSE TRUE TRUE protease) (Ubiquitin thioesterase 7) (Ubiquitin- specific-processing protease 7) Ubiquitin carboxyl-terminai hydrolase isozyme P15374 UCHL3 L3 (UCH-L3) (EC 3.4.19.12) (Ubiquitin 230 FALSE FALSE FALSE FALSE FALSE FALSE thioesterase L3) •J\ Ubiquitin carboxyl-terminai hydrolase isozyme L5 (UCH-L5) (EC 3.4.19.12) (Ubiquitin C- Q9Y5K5 UCHL5 329 TRUE TRUE TRUE FALSE TRUE TRUE terminal hydrolase UCH37) (Ubiquitin thioesterase L5) Ubiquitin conjugation factor E4 A (EC Q14139 UBE4A 2.3.2.27) (RING-type E3 ubiquitin transferase 1066 FALSE FALSE FALSE TRUE FALSE TRUE E4 A)

Ubiquitin recognition factor in ER-associated Q92890 UFD1 degradation protein 1 (Ubiquitin fusion 307 FALSE FALSE FALSE FALSE FALSE FALSE degradation protein 1) (UB fusion protein 1)

Ubiquitin thioesterase OTUB2 (EC 3.4.19.12) (Deubiquitinating enzyme OTUB2) (OTU Q96DC9 OTUB2 domain-containing ubiquitin aldehyde-binding 234 FALSE FALSE FALSE FALSE FALSE FALSE protein 2) (Otubain-2) (Ubiquitin-specific- processing protease OTUB2) Ubiquitin-40S ribosornal protein S27a (Ubiquitin carboxyl extension protein 80) P62979 RPS27A 156 FALSE FALSE FALSE FALSE FALSE FALSE [Cleaved into: Ubiquitin; 40S ribosornal protein S27a (Small ribosornal subunit protein eS31)] Ubiquitin-associated protein 2-like (Protein Q14157 UBAP2L 1087 FALSE FALSE FALSE FALSE FALSE FALSE NICE-4)

Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme P68036 UBE2L3 L3) (L-UBC) (UbcH7) (Ubiquitin carrier protein 154 FALSE FALSE FALSE FALSE FALSE FALSE L3) (Ubiquitin-conjugating enzyme E2-F1) (Ubiquitin-protein ligase L3)

Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) (Bendless-like ubiquitin-conjugating P61088 UBE2N enzyme) (E2 ubiquitin-conjugating enzyme N) 2 FALSE! FALSE! FALSE! FALSE FALSE! FALSE (Ubc13) (UbcH13) (Ubiquitin carrier protein N) (Ubiquitin-protein ligase N)

Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme S) (E2-EPF) (Ubiquitin carrier protein S) Q16763 UBE2S 222 FALSE TRUE FALSE FALSE FALSE FALSE (Ubiquitin-conjugating enzyme E2-24 kDa) (Ubiquitin-conjugating enzyme E2-EPF5) (Ubiquitin-protein ligase S) Ubiquitin-conjugating enzyme E2 variant 1 Q13404 UBE2V1 (UEV-1) (CROC-1) (TRAF6-regulated KK 147 FALSE FALSE FALSE FALSE FALSE FALSE activator 1 beta UevIA) Ubiquitin-conjugating enzyme E2 variant 2 (DDVit 1) (Enterocyte differentiation- associated factor 1) (EDAF-1) (Enterocyte Q15819 UBE2V2 145 FALSE FALSE FALSE FALSE FALSE FALSE differentiation-promoting factor 1) (EDPF-1) ( S2 homolog) (Vitamin D3-inducibie protein) P61960 UFM1 Ubiquitin-fold modifier 1 85 FALSE FALSE FALSE FALSE FALSE FALSE Ubiquitin-like modifier-activating enzyme 1 P2231 4 UBA1 (EC 6.2. 1.45) (Protein A 1S9) (Ubiquitin- 1058 FALSE FALSE FALSE FALSE FALSE FALSE activating enzyme E 1) Ubiquitin-like modifier-activating enzyme 5 (Ubiquitin-activating enzyme 5) (ThiFPI ) Q9GZZ9 UBA5 (UFM 1-activating enzyme) (Ubiquitin- FALSE FALSE FALSE FALSE FALSE FALSE activating enzyme E 1 domain-containing protein 1) Ubiquitin-like modifier-activating enzyme 6 (Ubiquitin-activating enzyme 6) (EC 6.2. 1.45) A0AVT1 UBA6 352 TRUE TRUE FALSE TRUE TRUE TRUE (Monocyte protein 4) (MOP-4) (Ubiquitin- activating enzyme E 1-like protein 2) (E1 -L2) Ubiquitin-like-conjugating enzyme ATG3 (EC Q9NT62 ATG3 6.3.2.-) (Auiophagy-reiated protein 3) (APG3- 3 14 FALSE FALSE TRUE FALSE FALSE FALSE ike) (hApg3) (Protein PC3-96) Ubiquitin-protein ligase E3C (EC 2.3.2.26) Q 5386 UBE3C (HECT-type ubiquitin transferase ESC) 1 83 FALSE FALSE FALSE FALSE FALSE FALSE (HectH2) UBX domain-containing protein 1 (SAPK Q04323 UBXN 1 substrate protein 1) (UBA/UBX 33 3 kDa 297 FALSE FALSE FALSE FALSE FALSE FALSE protein) UBX domain-containing protein 4 (Erasin) Q92575 UBXN4 508 FALSE FALSE FALSE TRU E TRUE TRUE (UBX domain-containing protein 2) UBX domain-containing protein 6 (UBX Q9BZV1 UBXN6 441 FALSE FALSE FALSE FALSE FALSE FALSE domain-containing protein 1) UDP-giucose 4-epimerase (EC 5 .1.3.2) (Galactowaldenase) (UDP-N- acetyigalaciosamine 4-epimerase) (UDP- Q 4376 GALE Ga!NAc 4-epimerase) (UDP-N- 348 FALSE TRUE FALSE FALSE FALSE FALSE acetylglucosamine 4-epimerase) (UDP- GlcNAc 4-epimerase) (EC 5 .1.3.7) (UDP- gaiactose 4-epimerase) UDP~giucose:glycoprotein glucosyliransferase 1 (UGT1) (hUGT1) (EC 2.4.1 -) (UDP- G9NYU2 UGGT1 FALSE FALSE FALSE TRUE FALSE TRUE Glc:glycoproiein glucosyliransferase) (UDP- glucose ceramicle g!ucosyltransferase-like 1)

UDP-N-acetylglucosamine-peptide N- acetylglucosaminy!transferase 0 kDa 0 15294 OGT subunit (EC 2.4. 1.255) (O-GlcNAc transferase FALSE FALSE FALSE FALSE FALSE FALSE subunit p 10) (O-linked N-acefylglucosamine transferase 110 kDa subunit) (OGT)

UHRF1-binding protein 1 (ICBP90-binding UHRF1 B Q6BDS2 protein 1) (Ubiquitin-like containing PHD and F L3 Ε A L Ξ F L3 Ε F LS Ε FAL Ξ FAL3 EE P 1 RING finger domains 1-binding protein 1) U P C P kinase (EC 2.7.4.14) (Deoxycytidyiaie kinase) (CK) (dCMP kinase) (Nucleoside-diphosphate kinase) (EC 2.7.4.6) P30085 C PK1 196 FALSE FALSE FALSE TRUE TRUE TRUE (Uridine monophosphate/cytidine monophosphate kinase) (UMP/CMP kinase) (UMP/CMPK) Uncharacterized protein C20orf24 (Rab5- Q9BUV8 C20orf24 137 FALSE TRUE FALSE FALSE FALSE FALSE interacting protein) (RIP5) Up-reguiated during skeletal muscle growth protein 5 (Diabetes-associated protein in Q96IX5 US G5 58 FALSE TRUE TRUE FALSE FALSE FALSE insulin-sensitive tissues) (HCV F- transactivated protein 2) Q9H7E9 C8orf33 UPF0488 protein C8orf33 229 FALSE FALSE FALSE FALSE TRUE FALSE C14orf16 UPF0568 protein C14orf166 (CLE7 homolog) Q9Y224 244 FALSE FALSE FALSE TRUE FALSE FALSE 6 (CLE) A6NDU8 C5orf51 UPF0600 protein C5orf51 294 FALSE FALSE FALSE FALSE FALSE FALSE Uridine 5'~monophosphate synthase (UIV3P synthase) [Includes: Orotate phosphoribosyltransferase (OPRT) 480 TRUE TRUE FALSE FALSE FALSE FALSE (OPRTase) (EC 2 .4.2 10); Orotidine 5'- phosphate decarboxylase (ODC) (EC 4.1 . 1 .23) (OMPdecase)]

UV excision repair protein RAD23 homolog B P54727 RAD23B (HR23B) (hHR23B) (XP-C repair- 409 FALSE FALSE FALSE TRUE FALSE FALSE complementing complex 58 kDa protein) (p58;

V-type proton ATPase catalytic subunit A (V- ATPase subunit A) (EC 3.6.3.14) (V-ATPase ATP6V1A 617 FALSE FALSE FALSE TRUE FALSE TRUE 69 kDa subunit) (Vacuolar ATPase isoform VA68) (Vacuolar proton pump subunit alpha)

V-type proton ATPase subunit B, brain isoform ATP6V1B (V-ATPase subunit B 2) (Endomembrane P21281 5 11 FALSE FALSE FALSE FALSE FALSE FALSE g ' - ' proton pump 58 kDa subunit) (H057) (Vacuolar proton pump subunit B 2)

V~type proton ATPase subunit G 1 (V-ATPase ATP6V1G subunit G 1) (V-ATPase 13 kDa subunit 1) 075348 118 FALSE FALSE FALSE FALSE FALSE FALSE 1 (Vacuolar proton pump subunit G 1) (Vacuolar proton pump subunit M16)

V-type proton ATPase subunit H (V-ATPase subunit H) (Nef-binding protein 1) (NBP1) Q9UI12 ATP6V1 H (Protein V A 13 homolog) (V-ATPase 50/57 483 FALSE FALSE FALSE TRUE FALSE FALSE kDa subunits) (Vacuolar proton pump subunit H) (Vacuolar proton pump subunit SFD)

Vacuolar ATPase assembly integral Q3ZAQ7 V A2 1 membrane protein V A2 1 (Myopathy with 101 TRUE TRUE FALSE FALSE FALSE FALSE excessive autophagy protein)

Vacuolar protein sorting-associated protein 327 TRUE FALSE FALSE FALSE FALSE FALSE 26A (Vesicle protein sorting 26A) (hVPS26) Vacuolar proiein sorting-associated protein 29 Q9UBQ0 VPS29 (hVPS29) (PEP1 homolog) (Vesicle protein 182 TRUE FALSE FALSE FALSE FALSE FALSE sorting 29) Vacuolar protein sorting-associated protein 35 Q96QK1 VPS35 (hVPS35) (Maternal-embryonic 3) (Vesicle 796 TRUE TRUE TRUE TRUE TRUE TRUE protein sorting 35) Vacuolar protein sorting-associated protein Q9H9H4 VPS37B 37B (hVps37B) (ESCRT-I complex subunit 285 FALSE FALSE FALSE FALSE FALSE FALSE VPS37B) Vacuolar protein sorting-associated protein 4A Q9UN37 VPS4A (EC 3.6.4.6) (Protein SKD2) (VPS4- 1) 437 FALSE FALSE FALSE FALSE FALSE FALSE (hVPS4) Vacuolar protein sorting-associated protein 52 Q8N1 B4 VPS52 homolog (SAC2 suppressor of actin mutations 723 FALSE FALSE FALSE FALSE FALSE FALSE 2-like protein) Vacuolar protein sorting-associated protein VTA1 homolog (Dopamine-responsive gene 1 Q9NP79 VTA1 307 TRUE TRUE FALSE FALSE TRUE TRUE protein) (DRG- 1) (LYST-interacting protein 5) (LIPS) (SKD1-binding protein 1) (SBP1)

Vacuolar protein-sorting-associated protein 25 (hVps25) (Dermal papilla-derived protein 9) Q9BRG1 VPS25 176 FALSE FALSE FALSE FALSE FALSE FALSE (ELL-associated protein of 20 kDa) (ESCRT- complex subunit VPS25)

Valine-tRNA iigase (EC 6.1 . 1 .9) (Protein P26640 VARS 1264 FALSE FALSE FALSE FALSE FALSE FALSE G7a) (Valyl-tRNA synthetase) (VaIRS) P50552 VASP Vasodilator-stimulated phosphoprotein (VASP) 380 FALSE FALSE FALSE FALSE FALSE FALSE Very long-chain acyl-CoA synthetase (VLACS) (VLCS) (EC 6.2.1 .-) (Fatty acid transport protein 2) (FATP-2) (Fatty-acid-coenzyme A SLC27A2 ligase, very long-chain 1) (Long-chain-fatty- 620 FALSE FALSE FALSE FALSE FALSE FALSE acid-CoA ligase) (EC 6.2.1 .3) (SoiLfte carrier family 27 member 2) (THCA-CoA ligase) (Very long-chain-fatty-acid-CoA ligase)

Very long-chain specific acyl-CoA ACADVL dehydrogenase, mitochondrial (VLCAD) (EC 655 TRUE FALSE FALSE TRUE TRUE FALSE 1.3.8.9) Very-long-chain (3R)-3-hydroxyacyi-CoA dehydratase 3 (EC 4.2.1.134) (3-hydroxyacyl- CoA dehydratase 3) (HACD3) (Butyrate- Q9PQ35 HACD3 3Θ2 F S ! F F ! FALSE TRUE TRUE induced protein 1) (B-ind1) (hB-ind1) (Protein- tyrosine phosphatase-iike A domain- containing protein 1) Very-long-chain 3-oxoacyl-CoA reductase (EC 1. 1 . 1 .330) ( 17-beta-hydroxysteroid dehydrogenase 12) (17-beta-HSD 12) (3- HSD17B1 Q53GQ0 ketoacyl-CoA reductase) (KAR) (Estradiol 1 - 312 FALSE FALSE FALSE FALSE FALSE FALSE beta-dehydrogenase 12) (EC 1. 1 . 1 .62) (Short chain dehydrogenase/reductase family 12C member 1) Very-long-chain enoyl-CoA reductase (EC Q9NZ01 TECR 1.3. .93) (Synaptic glycoprotein SC2) (Trans- 308 FALSE FALSE FALSE FALSE FALSE FALSE 2,3-enoyl-CoA reductase) (TER) Vesicle-associated membrane protein 2 P63027 VAMP2 16 FALSE FALSE FALSE TRUE FALSE FALSE (VAMP-2) (Synaptobrevin-2) Vesicle-associated membrane protein- assoc a ed protein A (VAMP-A) (VAMP- Q9P0L0 VAPA 249 FALSE FALSE FALSE TRUE TRUE TRUE assoc a ed protein A) (VAP-A) (33 kDa VAMP- associated protein) (VAP-33) Vesicle-associated membrane protein- associated protein B/C (VAMP-B/VAMP-C) 095292 VAPB 243 FALSE FALSE FALSE FALSE FALSE FALSE (VAMP-associated protein B/C) (VAP-B/VAP- C) Vesicle-fusing ATPase (EC 3.6.4 6) (N- ethylmaleimide-sensitive fusion protein) (NEM- P46459 NSF TRUE FALSE FALSE TRUE FALSE FALSE sensitive fusion protein) (Vesicular-fusion protein NSF) Vesicle-trafficking protein SEC22b (ER-Golgi SNARE of 24 kDa) (ERS-24) (ERS24) (SEC22 075396 SEC22B 215 FALSE FALSE FALSE FALSE FALSE FALSE vesicle-trafficking protein homolog B) (SEC22 vesicle-trafficking protein-like 1) Vesicular integral-membrane protein VIP36 (Glycoprotein GP36b) (Lectin mannose- Q12907 LMAN2 356 TRUE TRUE FALSE FALSE FALSE FALSE binding 2) (Vesicular integral-membrane protein 36) (V1P36) Vigilin (High density lipoprotein-binding •J\ Q00341 HDLBP 1268 TRUE TRUE FALSE FALSE FALSE FALSE -4 protein) (HDL-binding protein) Vitamin K epoxide reductase complex subunit Q9BQB6 VKORC1 1 (EC 1.17.4.4) (Vitamin K 1 2,3-epoxide 163 FALSE TRUE FALSE FALSE FALSE FALSE reductase subunit 1) Voltage-dependent anion-selective channel protein 1 (VDAC-1) (hVDACI) (Outer P21796 VDAC1 mitochondrial membrane protein porin 1) 283 FALSE FALSE FALSE FALSE FALSE FALSE (Plasmalemmal porin) (Porin 3 1HL) (Porin 3 1HM) Voltage-dependent anion-selective channel Ρ45880 protein 2 (VDAC-2) (hVDAC2) (Outer 294 FALSE FALSE FALSE FALSE FALSE FALSE mitochondrial membrane protein porin 2)

Voltage-dependent anion-selective channel Q9Y277 VDAC3 protein 3 (VDAC-3) (hVDAC3) (Outer 283 FALSE FALSE FALSE FALSE FALSE FALSE mitochondrial membrane protein porin 3) WASH complex subunit 4 {Strurnpe!lin and Q2 389 W/ASHC4 WASH-interacting protein) (SWiP) (WASH 1173 FALSE FALSE FALSE FALSE FALSE FALSE complex subunit SWIP) W D repeat and HMG-box DNA-binding protein 075717 WDHD1 1 (Acidic nucleoplasms DNA-binding protein 1129 FALSE FALSE FALSE FALSE FALSE FALSE 1) (And-1) W D repeat-containing protein 1 (Actin- 075083 WDR1 6 6 FALSE FALSE FALSE FALSE FALSE FALSE interacting protein 1) (AIP1) (NORI-1) Q9UNX4 WDR3 W D repeat-containing protein 3 943 TRUE TRUE TRUE FALSE FALSE FALSE W D repeat-containing protein 36 (T-ceil G8NI36 WDR36 activation W D repeat-containing protein) (TA- 951 FALSE FALSE FALSE FALSE FALSE FALSE WDRP) W D repeat-containing protein 43 (U3 small Q15061 WDR43 677 TRUE FALSE TRUE FALSE FALSE TRUE nucleolar RNA-associated protein 5 homolog) W D repeat-containing protein 46 (WD repeat- 015213 WDR46 610 FALSE F S F FALSE. TRUE containing protein BING4) W D repeat-containing protein 5 (B P2- •J\ P61964 WDR5 334 FALSE F S F TRUE FALSE FALSE induced 3-kb gene protein) W D repeat-containing protein 75 (U3 small Q8IWA0 WDR75 nucleolar RNA-associated protein 830 FALSE FALSE FALSE FALSE FALSE FALSE homolog) WD repeat-containing protein 82 (Protein Q6UXN9 WDR82 313 TRUE FALSE FALSE TRUE TRUE TRUE TMEM1 3) (Swd2) WD40 repeat-containing protein S U1 (Sr u- 1 suppressor of mec-8 and unc-52 protein Q2TAY7 SMU1 homolog) [Cleaved into: WD40 repeat- 513 TRUE FALSE FALSE TRUE TRUE TRUE containing protein SMU1, N-terminaliy processed] X-ray repair cross-complementing protein 5 (EC 3.6.4.-) (86 kDa subunit of K antigen) (ATP-depenclent DNA helicase 2 subunit 2) (ATP-dependent DNA helicase 80 kDa subunit) (CTC box-binding factor 85 kDa subunit) (CTC85) (CTCBF) (DNA repair P13010 XRCC5 732 FALSE FALSE FALSE FALSE FALSE FALSE protein XRCC5) (Ku80) (Ku86) (Lupus Ku autoantigen protein p86) (Nuclear factor IV) (Thyroid-lupus autoantigen) (TLAA) (X-ray repair complementing defective repair in Chinese hamster cells 5 (doubie-strand-break rejoining))

X-ray repair cross-complementing protein 6 (EC 3.6.4.-) (EC 4.2.99.-) (5'-deoxyribose-5- phosphate lyase Ku70) (5'-dRP lyase Ku70) (70 kDa subunit of Ku antigen) (ATP- dependent DNA helicase 2 subunit 1) (ATP- dependent DNA helicase II 70 kDa subunit) P12956 XRCC6 609 FALSE FALSE FALSE FALSE FALSE FALSE (CTC box-binding factor 75 kDa subunit) (CTC75) (CTCBF) (DNA repair protein XRCC6) (Lupus Ku autoantigen protein p70) (Ku70) (Thyroid-lupus autoantigen) (TLAA) (X- ray repair complementing defective repair in Chinese hamster cells 6)

Xaa-Pro aminopeptidase 1 (EC 3.4.1 .9) (Aminoacyiproline aminopeptidase) (Cytosoiic Q9NQW7 XPNPEP1 aminopeptidase P) (Soluble aminopeptidase 623 FALSE FALSE FALSE TRUE TRUE TRUE P) (sAmp) (X-Pro aminopeptidase 1) (X-pro y aminopeptidase 1, soluble)

Y-box-binding protein 3 (Cold shock domain- Pi 6989 YBX3 containing protein A) (DNA-binding protein A) 372 FALSE FALSE FALSE FALSE FALSE FALSE (Single-strand DNA-binding protein NF-G B) ΥΤΗ domain-containing family protein 1 Q9BYJ9 YTHDF1 (Dermatomyositis associated with cancer 559 FALSE FALSE FALSE FALSE FALSE FALSE putative autoantigen 1) (DACA-1) YTH domain-containing family protein 2 (CLL- associated antigen KW-14) (High-glucose- Q9Y5A9 YTHDF2 579 FALSE FALSE FALSE FALSE FALSE FALSE regulated protein 8) (Renai carcinoma antigen NY-REN-2) Zinc finger CCCH domain-containing protein 075152 ZC3H1 1A 810 FALSE FALSE FALSE FALSE FALSE FALSE 11A Zinc finger CCCH domain-containing protein 14 (Mammalian suppressor of tau patboiogy- Q6PJT7 ZC3H14 736 FALSE FALSE FALSE TRUE TRUE FALSE 2) (MSUT-2) (Renal carcinoma antigen NY- REN-37) Zinc finger CCCH domain-containing protein 5 (DRG family-regulatory protein 1) (Likely Q8WU90 ZC3H15 426 FALSE FALSE FALSE FALSE FALSE FALSE ortholog of mouse immediate early response erythropoietin 4) Zinc finger CCCH domain-containing protein Q86V 9 ZC3H18 953 FALSE FALSE FALSE FALSE FALSE FALSE 18 (Nuclear protein NHN1) Zinc finger CCCH-type antiviral protein 1 (ADP- ribosyitransferase diphtheria toxin-like 13) Q7Z2W4 ZC3HAV1 (ARTD13) (Zinc finger CCCH domain- 902 FALSE FALSE FALSE FALSE FALSE FALSE containing protein 2) (Zinc finger antiviral protein) (ZAP) Zinc finger HIT domain-containing protein 2 Q9UHR6 ZNH1T2 403 FALSE TRUE FALSE FALSE FALSE FALSE (Protein FON) E3 ubiquitin-protein ligase ZNF598 (EC Q86UK7 ZNF598 904 FALSE FALSE FALSE TRUE FALSE FALSE 2.3.2.27) (Zinc finger protein 598) Zinc finger protein ubi-d4 (Apoptosis response zinc finger protein) (BRG1 -associated factor Q92785 DPF2 391 TRUE TRUE FALSE FALSE FALSE FALSE 45D) (BAF45D) (D4, zinc and double PHD fingers family 2) (Protein requiem) Zinc finger Ran-binding domain-containing 095218 ZRANB2 protein 2 (Zinc finger protein 265) (Zinc finger, 330 FALSE FALSE FALSE TRUE FALSE FALSE splicing) Zinc finger RNA-binding protein (hZFR) (M- Q96KR1 ZFR 1074 FALSE FALSE FALSE FALSE FALSE FALSE phase phosphoprotein homo!og) Zinc phosphodiesterase ELAC protein 2 (EC 3.1 .26 11) (E aC homolog protein 2) (Heredity Q9BQ52 ELAC2 prostate cancer protein 2) (Ribonuclease Z 2) 826 FALSE FALSE FALSE FALSE FALSE FALSE (RNase Z 2) (tRNA 3 endonuciease 2) (tRNase Z 2) Zinc transporter SLC39A7 (Histidine-rich membrane protein e4) (Really interesting Q92504 SLC39A7 469 TRUE TRUE TRUE FALSE FALSE FALSE new gene 5 protein) (Solute carrier family 39 member 7) (Zrt-, Irt-like protein 7) (ZIP7) Q15942 ΖΥΧ Zyxin (Zyxin-2) 572 FALSE FALSE FALSE FALSE FALSE FALSE M-phase-specific PLK1 -interacting protein Q8TAP9 MPLKIP 179 #N/A #N/A #N/A FALSE FALSE FALSE (TTD non-photosensitive 1 protein) Tubulin beta-4A chain (Tubulin 5 beta) Ρ04350 TUBB4A 444 #N/A #N/A #N/A F LS Ε F L Ξ F LS EE (Tubulin beta-4 chain) Integrator complex subunit 3 (Int3) (SOSS complex subunit A) (Sensor of single-strand Q68E01 NTS3 1043 #N/A #N/A #N/A FALSE TRUE FALSE DNA complex subunit A) (SOSS-A) (Sensor of ssDNA subunit A) Doubie-strand-break repair protein rad21 060216 RAD21 homolog (hHR21) (Nuclear matrix protein 1) 631 #N/A #N/A #N/A TRUE TRUE FALSE (NXP-1) (SCC1 homolog)

Serine/threonine-protein kinase Nek9 (EC 2.7.1 1.1) (Ner kinase) (Never in mitosis A- Q8TD19 ΝΕΚ9 979 #N/A #N/A #N/A FALSE FALSE FALSE related kinase 9) (NimA-related protein kinase 9) (NimA-related kinase 8) (Nek8)

Protein NEDD1 (Neural precursor cell G8NHV4 NEDD1 expressed developmentally down-regulated 660 #N/A #N/A #N/A TRUE TRUE FALSE protein 1) (NEDD-1) Adenosine deaminase (EC 3.5.4.4) Ρ00813 ADA 363 #N/A #N/A #N/A FALSE FALSE FALSE (Adenosine aminohydroiase) Secretory carrier-associated membrane 0 15 126 SCA P1 protein 1 (Secretory carrier membrane protein 338 #N/A #N/A #N/A FALSE FALSE FALSE 1) Spectrin alpha chain, non-erythrocytic 1 Q13813 SPTAN1 (A pha- spectrin) (Fodrin alpha chain) 2472 #N/A #N/A #N/A FALSE FALSE FALSE (Spectrin, non-erythroid alpha subunit) Dihydropyrimidinase-reiated protein 2 (DRP-2) (Coilapsin response mediator protein 2) Q16555 DPYSL2 572 #N/A #N/A #N/A FALSE FALSE FALSE (CRMP-2) (N2A3) (Unc-33-like phosphoprotein 2) (ULIP-2) 043660 PLRG1 Pleiotropic regulator 1 514 #N/A #N/A #N/A FALSE FALSE FALSE Rho GDP-dissociation inhibitor 2 (Rho GDI 2) P52566 ARHGDIB 2 1 #N/A #N/A #N/A F LS Ε F L Ξ F LS EE (Ly-GDI) (Rho-GDi beta) Transcription elongation factor SPT6 (hSPT6) Q7KZ85 H (Histone chaperone suppressor of Ty6) (Tat- 1726 #N/A #N/A #N/A TRUE FALSE FALSE cotransactivator 2 protein) (Tat~CT2 protein) Tyrosine-protein phosphatase non-receptor P17706 PTPN2 type 2 (EC 3 1.3.48) (T-ce protein-tyrosine 415 #N/A #N/A #N/A FALSE FALSE FALSE phosphatase) (TCPTP) HLA class histocompatibility antigen, A-3 P04439 HLA-A 365 #N/A #N/A #N/A FALSE FALSE FALSE alpha chain ( HC class antigen A*3)

Unconventional myosin-lg [Cleaved into: Minor B0I1T2 1Y01G 1018 #N/A #N/A #N/A FALSE FALSE FALSE histocompatibility antigen HA-2 (mHag HA-2)]

AT-rich interactive domain-containing protein A (ARID domain-containing protein 1A) (B120) (BRG1 -associated factor 250) (BAF250) (BRG1 -associated factor 250a) 014497 ARID1A (BAF250A) (Osa homoiog 1) (hOSA1) (SWI- 2285 #N/A #N/A #N/A FALSE FALSE FALSE ike protein) (SWI/SNF complex protein p270) (SWI/SNF-related, matrix-associated, actin- dependent regulator of chromatin subfamily F member 1) (hELD) Actin-reiaied protein 2/3 cornpiex subunit 1A Q92747 ARPC1A 370 #N/A #N/A #N/A TRUE FALSE FALSE (SOP2-like protein) CDKN2AI CDKN2A-interacting protein (Collaborator of Q9NXV6 580 #N/A #N/A #N/A TRUE FALSE FALSE Ρ ARF) Vascular endothelial zinc finger 1 (Putative Q141 19 VEZF1 transcription factor DB1) (Zinc finger protein 521 #N/A #N/A #N/A FALSE FALSE FALSE 161) TATA-binding protein-associated factor 1 2 (EC 3.6.4.-) (ATP-dependent helicase BTAF1) 014981 BTAF1 (B-TFi!D transcription factor-associated 170 1849 #N/A #N/A #N/A FALSE FALSE FALSE kDa subunit) (TAF(i!)170) (TBP-associated factor 172) (TAF- 172) ADP-ribosylation factor-like protein 8A (ADP- ribosylation factor-like protein 10B) (Novel Q96B 9 ARL8A 186 #N/A #N/A #N/A FALSE FALSE FALSE small G protein indispensable for equal chromosome segregation 2) Annexin A6 (67 kDa caleiectrin) (Annexin VI) (Annexin-6) (Calphobindin-ll) (CPB-ii) Ρ08133 ΑΝΧΑ6 673 #N/A #N/A #N/A FALSE FALSE FALSE (Chromobindin-20) (Lipocortin VI) (Protein Hi) (p68) (p70)

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma- 1 (EC 3.1 .4.1 1) (PLC-148) (Phosphoinositide phospholipase C 1290 #N/A #N/A #N/A FALSE FALSE FALSE gamma-1) (Phospholipase C-H) (PLC-II) (Phospholipase C-gamma-1) (PLC-gamma-1)

Selenocysteine-specific elongation factor P57772 EEFSEC (Elongation factor sec) (Eukaryotic elongation 596 #N/A #N/A #N/A FALSE FALSE FALSE factor, selenocysteine-tRNA-specific)

Gamma-interferon-inducibie protein 16 (lfi-16) Q16666 IFI16 (interferon-inducible myeloid differentiation 785 #N/A #N/A #N/A FALSE FALSE FALSE transcriptional activator) Proteasome activator complex subunii 1 ( S regulator complex subunit alpha) (REG-alpha) (Activator of multicatalytic protease subunit 1) 'Jb r Vb ;. , , , , 249 #N/A #N/A #N/A TRUE TRUE TRUE (Interferon gamma up-regulated - 5 1 protein) (!GUP - 5 1 11) (Proteasome activator 28 subunit alpha) (PA28a) (PA28aipha)

060234 GMFG G ia maturation factor gamma (GMF-gamma) 142 #N/A #N/A #N/A FALSE FALSE FALSE

T-ce surface antigen CD2 (Erythrocyte receptor) (LFA-2) (LFA-3 receptor) (Rosette P06729 CD2 351 #N/A #N/A #N/A TRUE TRUE TRUE receptor) (T-cell surface antigen TH/Leu-5) (CD antigen CD2) ARF GTPase-activating protein G T2 (ARF GAP GIT2) (Cool-interacting tyrosine- Q14161 GIT2 phosphorylated protein 2) (CAT-2) (CAT2) (G 759 #N/A #N/A #N/A FALSE FALSE FALSE protein-coupled receptor kinase-interactor 2) (GRK-interacting protein 2) COP9 signalosome complex subunit 3 (SGN3) Q9UNS2 COPS3 (Signalosome subunit 3) (JAB1 -containing 423 #N/A #N/A #N/A FALSE FALSE FALSE signalosome subunit 3) Tyrosine-protein kinase Lck (EC 2.7.10.2) (Leukocyte C~terminai Src kinase) (LSK) (Lymphocyte cell-specific protein-tyrosine P06239 LCK 509 #N/A #N/A #N/A FALSE FALSE FALSE kinase) (Protein YT16) (Proto-oncogene Lck) (T cell-specific protein-tyrosine kinase) (p56-

Na(+)/H(+) exchange regulatory cofacfor NHE- RF1 (NHERF-1) (Ezrin-radixin-moesin-binding phosphoprotein 50) (EBP50) (Regulatory SLC9A3R cofactor of Na(+)/H(+) exchanger) (Sodium- 358 #N/A #N/A #N/A FALSE FALSE FALSE hydrogen exchanger regulatory factor 1) (Solute carrier family 9 isoform A3 regulatory factor 1) Omega-amidase NIT2 (EC 3.5.1 .3) (Nitrilase Q9NQR4 ΝΙΤ2 276 #N/A #N/A #N/A FALSE FALSE FALSE homo!og 2) Differentially expressed in FDCP 6 homo!og Q9H4E7 DEF6 631 #N/A #N/A #N/A FALSE FALSE FALSE (DEF-6) (IRF4-binding protein) Glucocorticoid receptor (GR) (Nuclear Ρ04150 NR3C1 777 #N/A #N/A #N/A FALSE FALSE FALSE receptor subfamily 3 group C member 1) SWi/SNF-reiated matrix-associated actin- dependent regulator of chromatin subfamily D SMARCD member 1 (60 kDa BRG-1/Brm-associated Q96G 5 515 #N/A #N/A #N/A FALSE FALSE FALSE 1 factor SLfbunit A) (BRG1 -associated factor 60A) (BAF60A) (SWI/SNF complex 60 kDa subunit) T-celi surface glycoprotein CDS epsiion chain Ρ07766 CD3E (T-celi surface antigen T3/Leu-4 epsiion chain) 207 #N/A #N/A #N/A TRUE TRUE TRUE (CD antigen CD3e) ATP synthase F(0) complex subunit C3, mitochondrial (ATP synthase lipid-binding protein) (ATP synthase proteolipid P3) (ATP Ρ48201 ATP5G3 142 #N/A #N/A #N/A FALSE F F synthase proton-transporting mitochondrial F(0) complex subunit C3) (ATPase protein 9) (ATPase subunit c) Q6NXE6 ARIV3C8 Armadillo repeat-containing protein 6 501 #N/A #N/A #N/A FALSE TRUE FALSE Rho GTPase-activating protein 4 (Rho-GAP ARHGAP Ρ98171 hematopoietic protein C1) (Rho-type GTPase- 946 #N/A #N/A #N/A FALSE FALSE FALSE 4 activating protein 4) (p1 15) TRAF3IP TRAF3-interacfing JNK-activating modulator Q9Y228 551 #N/A #N/A #N/A TRUE TRUE FALSE 3 (TRAFS-interacting protein 3) Vacuolar protein sorting-associated protein Q709C8 VPS13C 3753 #N/A #N/A #N/A FALSE FALSE FALSE 13C GTPase A P family member 1 (Immunity- Q8WWP7 GIMAP1 306 #N/A #N/A #N/A FALSE FALSE FALSE associated protein 1) (hIMAPI) Arf-GAP with coiled-coil, ANK repeat and PH Q15027 ACAP1 domain-containing protein 1 (Centaurin-beta- 740 #N/A #N/A #N/A TRUE TRUE TRUE 1) (Cnt-b1)

FAN Fanconi anemia group protein (Protein FACi) 1328 #N/A #N/A #N/A FALSE TRUE TRUE Gamma-enolase (EC 4.2 1. ) (2~phospho~D~ P09104 EN02 glyceraie hydro-lyase) (Eno!ase 2) (Neural 434 #N/A #N/A #N/A FALSE FALSE FALSE enolase) (Neuron-specific enolase) (NSE)

ARHGAP 0 s ~ te 5 [Cleaved Q92619 into: Minor histocompatibility antigen HA- 1 136 #N/A #N/A #N/A TRUE TRUE TRUE (mHag HA-1)] Q69YN2 CWF19L1 CWF19-iike protein 1 (C19L1) 538 #N/A #N/A #N/A TRUE TRUE TRUE

N PSNAP Q9BPW8 Protein NipSnap homolog 1 (NipSnapl) 284 #N/A #N/A #N/A FALSE FALSE FALSE CD99 antigen (12E7) (E2 antigen) (Protein CD99 MIC2) (T-cell surface glycoprotein E2) (CD 185 #N/A #N/A #N/A TRUE TRUE FALSE antigen CD99) Polyadenylate-binding protein-interacting protein 2 (PABP-interacting protein 2) (PAIP- Q9BPZ3 PAIP2 127 #N/A #N/A #N/A FALSE FALSE FALSE 2) (Poly(A)-binding protein-interacting protein

Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member P33527 ABCC1 1531 #N/A #N/A #N/A FALSE FALSE FALSE 1) (Leukotriene C(4) transporter) (LTC4 transporter) Splicing factor, arginine/serine-rich 19 (SR- related C-terminal domain-associated factor 1) (SR-related and CTD-associated factor 1) (SR- Q9H7N4 SCAF1 1312 #N/A #N/A #N/A FALSE FALSE FALSE reiated-CTD-associated factor) (SCAF) (Serine arginine-rich pre-mRNA splicing factor SR-A1) (SR-A1) Methylated-DNA-protein-cysteine methyltransferase (EC 2.1 . 1 .63) (6-0- P16455 MGMT methylguanine-DNA methyltransferase) 2 7 #N/A #N/A #N/A FALSE FALSE FALSE (MGMT) (O-6-methylguanine-DNA- alkyitransferase) Mitogen-aciivated protein kinase kinase kinase kinase 4 (EC 2 7. 1.1) (HPK/GCK-like 095819 kinase HGK) (MAPK/ERK kinase kinase 1239 #N/A #N/A #N/A FALSE FALSE FALSE kinase 4) ( EK kinase kinase 4) (MEKKK 4) (Nck-interacting kinase) Histone chaperone ASF1A (Anti-silencing function protein 1 homoiog A) (hAsfl) Q9Y294 ASF1A #N/A #N/A FALSE FALSE FALSE (hAsfla) (CCG1 -interacting factor A) (CIA) (hCIA)

Rabankyrin-5 (Rank-5) (Ankyrin repeat and Q9P2R3 ANKFY1 FYVE domain-containing protein 1) (Ankyrin 1169 #N/A #N/A #N/A FALSE F F repeats hooked to a zinc finger motif) NudC domain-containing protein 1 (Chronic Q96RS6 NUDCD1 myelogenous leukemia tumor antigen 66) 583 #N/A #N/A #N/A FALSE TRUE FALSE (Tumor antigen C L66) Dynein assembly factor 5 , axonemal (HEAT Q86Y56 DNAAF5 855 #N/A #N/A #N/A FALSE FALSE FALSE repeat-containing protein 2)

Q27J81 INF2 Inverted formin~2 (HBEBP2-binding protein C) 1249 #N/A #N/A #N/A FALSE FALSE FALSE T-cell surface glycoprotein CDS zeta chain (T- Ρ20963 CD247 cell receptor T3 zeta chain) (CD antigen 164 #N/A #N/A #N/A FALSE FALSE FALSE CD247) Ena/VASP-like protein (Ena/vasodilator- G9UI08 EVL 416 #N/A #N/A #N/A FALSE FALSE FALSE stimuiated phosphoprotein-iike) Methyl-CpG-binding domain protein 1 (CXXC- type zinc finger protein 3) (Methyl-CpG- Q9UIS9 605 #N/A #N/A #N/A FALSE FALSE FALSE binding protein MBD1) (Protein containing methyl-CpG-binding domain 1) Q86X76 NIT1 Nitriiase homoiog 1 (EC 3.5.-.-) 327 #N/A #N/A #N/A FALSE FALSE FALSE Mycophenolic acid acyl-glucuronide esterase, mitochondrial (EC 3.1.1 .93) (Alpha/beta Q9NUJ1 ABHD10 306 #N/A #N/A #N/A TRUE FALSE FALSE hydrolase domain-containing protein 10) (Abhydrolase domain-containing protein 10) Diacylgiycero! kinase alpha (DAG kinase alpha) (EC 2 7.1.107) (80 kDa diacylgiycero! P23743 DGKA 735 #N/A #N/A #N/A FALSE FALSE FALSE kinase) (Diglyceride kinase alpha) (DGK- alpha)

Leukotriene A-4 hydrolase (LTA-4 hydrolase) P09960 LTA4H 6 1 #N/A #N/A #N/A TRUE TRUE FALSE (EC 3.3.2.6) (Leukotriene A(4) hydrolase)

Disintegrin and metalloproteinase domain- containing protein 10 (ADAM 10) (EC 014672 ADAM 10 3.4.24.81) (CDw1 56) (Kuzbanian protein 748 #N/A #N/A #N/A FALSE FALSE TRUE homolog) (Mammalian disintegrin- meta!!oprotease) (CD antigen CD156c) 043379 WDR62 W D repeat-containing protein 62 1518 #N/A #N/A #N/A ∆ FALSE Voltage-gated potassium channel subunii beta- Q13303 KCNAB2 2 (EC 1. 1 .1.-) (K(+) channel subunit beta-2) 367 #N/A #N/A #N/A TRUE FALSE TRUE (Kv-beta-2) (hKvbeta2)

Chromobox protein homolog 1 (HPI Hsbeta) (Heterochromatin protein 1 homolog beta) Ρ83916 CBX1 185 #N/A #N/A #N/A FALSE FALSE FALSE (HP1 beta) (Heterochromatin protein p25) (M31) (Modifier 1 protein) (p25beta)

Ribose-phosphate pyrophosphokinase 2 (EC Ρ 11908 PRPS2 2.7.6.1) (PPRibP) (Phosphoribosyi 318 #N/A #N/A #N/A FALSE FALSE FALSE pyrophosphate synthase II) (PRS- )

Immunoglobulin-binding protein 1 (B-ce signal transduction molecule alpha 4) (Protein Ρ78318 GBP1 alpha-4) (CD79a-binding protein 1) (Protein 339 #N/A #N/A #N/A FALSE FALSE FALSE phosphatase 2/4/6 regulatory subunit) (Renal carcinoma antigen NY-REN-16) Bromodomain adjacent to zinc finger domain protein A (ATP-dependent chromatin- remode!ing protein) (ATP-utiiizing chromatin Q9NRL2 BAZ1A assembly and remodeling factor 1) (hACF1) 1556 #N/A #N/A #N/A FALSE FALSE FALSE (CHRAC subunit ACF1) (Williams syndrome transcription factor-related chromatin- remodeling factor 180) (WCRF180) (bWALpl)

Beta-catenin-like protein 1 (Nuclear- Q8WYA6 CTNNBL1 associated protein) (NAP) (Testis 563 #N/A #N/A #N/A FALSE TRUE FALSE development protein NYD-SP19) P55327 TPD52 Tumor protein D52 (Protein N8) 224 #N/A #N/A #N/A FALSE FALSE FALSE Protein RTF2 homolog (Replication Q9BY42 RTFDC1 iermination factor 2 domain-containing protein 306 #N/A #N/A #N/A TRUE TRUE FALSE 1) Lymphoid enhancer-binding factor 1 (LEF-1)

» Q9UJU2 LEF1 (T cell-specific transcription factor 1-alpha) 399 #N/A #N/A #N/A FALSE FALSE FALSE (TCF1 -alpha) General transcription factor II F subunit 1 (General transcription factor I F 74 kDa P35269 GTF2F1 subunit) (Transcription initiation factor II F 517 #N/A #N/A #N/A TRUE FALSE FALSE subunit alpha) (TFIIF-alpha) (Transcription initiation factor RAP74) SUN domain-containing protein 2 (Protein unc- Q9UH99 SUN2 84 homolog B) (Rab5-inferacting protein) 717 #N/A #N/A #N/A TRUE TRUE FALSE (RabSIP) (Sad1/unc-84 protein-like 2)

SH2 domain-containing protein 1A (Duncan disease SH2-protein) (Signaling lymphocytic 060880 SH2D1A activation molecule-associated protein) (SLAM- 128 #N/A #N/A #N/A TRUE FALSE TRUE associated protein) (T-cell signal transduction molecule SAP) Plasma membrane calcium-transporting ATPase 4 (PMCA4) (EC 3.6.3.8) (Matrix- P23634 ATP2B4 remodeling-associated protein 1) (Plasma 1241 #N/A #N/A #N/A FALSE FALSE FALSE membrane calcium ATPase isoform 4) (Plasma membrane calcium pump isoform 4)

Serine/threonine-protein kinase 24 (EC 2.7.1 1.1) (Mammalian STE20-like protein kinase 3) (MST-3) (STE20-like kinase ST3) [Cleaved into: Serine/threonine-protein kinase Q9Y6E0 STK24 24 36 kDa subunit (Mammalian STE20-like 443 #N/A #N/A #N/A TRUE TRUE FALSE protein kinase 3 N-terminal) (MST3/N); Serine/threonine-protein kinase 24 2 kDa subunit (Mammalian STE20-like protein kinase 3 C-terminal) (MST3/C)]

Amyloid beta A4 precursor protein-binding family B member 1-interacting protein (APBB1- interacting protein 1) (Proline-rich EVH1 Iigand Q7Z5R6 APBB1IP 1) (PREL-1) (Proline-rich protein 73) (Rap1- 666 #N/A #N/A #N/A FALSE FALSE FALSE GTP-interacting adapter molecule) (RIAM) (Retinoic acid-responsive proline-rich protein 1) (RARP-1) Importin subunit aipha-4 (importin alpha Q2) OQ0505 KPNA3 (Qip2) (Karyopherin subunit alpha-3) (SRP1- 521 #N/A #N/A #N/A FALSE FALSE FALSE gamma) Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1 149) (1- phosphatidylinositoi 5-phosphate 4~kinase 2- alpha) (Diphosphoinositide kinase 2-alpha) P48426 PIP4K2A (PIP5KNI) (Phosphatidylinositol 5-phosphate 4- 406 #N/A #N/A #N/A FALSE TRUE TRUE kinase type alpha) (PI(5)P 4-kinase type II alpha) (PIP4Kil-aipha) (Ptdlns(4)P-5-kinase B isoform) (Ptdlns(4)P-5-kinase C isoform) (Ptdins(5)P~4~kinase isoform 2-aipha)

Formin-like protein 1 (CLL-associated antigen 095466 F NL1 1100 #N/A #N/A #N/A TRUE TRUE TRUE KW-13) (Leukocyte formin) Poly(A) RNA polymerase, mitochondrial (PAP) (EC 2.7.7.19) (PAP-associated domain- Q9NW4 TPAP containing protein 1) (Polynucleotide 582 #N/A #N/A #N/A FALSE FALSE TRUE adenylyltransferase) (Terminal uridyiyitransferase 1) (TUTase 1) (mtPAP)

Engulfment and cell motility protein 1 (Protein Q92556 EL 0 1 727 #N/A #N/A #N/A FALSE FALSE FALSE ced-12 homolog) Vacuolar protein sorting-associated protein Q4G0F5 VPS26B 336 #N/A #N/A #N/A FALSE FALSE FALSE 26B (Vesicle protein sorting 26B) Dipeptidyl peptidase 1 (EC 3.4.14.1) (Cathepsin C) (Cathepsin J) (Dipeptidyl peptidase ) (DPP-I) (DPPi) (Dipeptidyl transferase) [Cleaved into: Dipeptidyl peptidase 1 exclusion domain chain P53634 CTSC 463 #N/A #N/A #N/A FALSE FALSE FALSE (Dipeptidyl peptidase exclusion domain chain); Dipeptidyl peptidase 1 heavy chain (Dipeptidyl peptidase heavy chain); Dipeptidyl peptidase 1 light chain (Dipeptidyl peptidase I light chain)]

Q96PZ2 FAM1 11A Protein FA 11A 6 11 #N/A #N/A #N/A FALSE TRUE FALSE Tyrosine-protein kinase ZAP-70 (EC 2 7. 0.2) P43403 ZAP70 (70 kDa zeta-chain associated protein) (Syk- 6 19 #N/A #N/A #N/A FALSE FALSE FALSE re!ated tyrosine kinase)

Unconventional myosin-XVI Ia (Molecule 4 . associated with JAK3 N-terminus) (MAJN) 2054 #N/A #N/A #N/A FALSE TRUE TRUE (Myosin containing a PDZ domasn) (Surfactant protein receptor SP-R2 10) (SP-R2 10)

Elongation of very long chain fatty acids protein 5 (EC 2.3. 1.199) (3-keto acyi-CoA synthase ELOVL5) (ELOVL fatty acid Q9NYP7 ELOVL5 elongase 5) (ELOVL FA eiongase 5) (Fatty 299 #N/A #N/A #N/A FALSE FALSE FALSE acid eiongase 1) (hELOI ) (Very long chain 3- ketoacyl-CoA synthase 5) (Very long chain 3- oxoacyl-CoA synthase 5)

DNA-binding protein karos ( karos family zinc Q13422 IKZF1 finger protein 1) (Lymphoid transcription factor 5 19 #N/A #N/A #N/A FALSE FALSE FALSE LyF-1 ) Glycogen [starch] synthase, muscle (EC P 13807 GYS1 737 #N/A #N/A #N/A FALSE FALSE FALSE 2.4. 1.11) Retinoblastoma-associated protein (p1 05~Rb) P06400 RB1 928 #N/A #N/A #N/A FALSE FALSE FALSE (pRb) (Rb) (pp1 10) Lymphocyte cytosolic protein 2 (SH2 domain- Q13094 LCP2 containing leukocyte protein of 76 kDa) (SLP- 533 #N/A #N/A #N/A FALSE FALSE FALSE 76 tyrosine phosphoprofein) (SLP76)

Antigen peptide transporter 1 (APT1 ) (ATP- binding cassette sub-family B member 2) (Peptide supply factor 1) (Peptide transporter Q0351 8 TAP1 PSF 1) (PSF-1 ) (Peptide transporter TAP 1) 808 #N/A #N/A #N/A FALSE TRUE TRUE (Peptide transporter involved in antigen processing 1) (Really interesting new gene 4 protein) Interferon regulatory factor 2~binding protein 2 Q7Z5L9 1RF2BP2 587 #N/A #N/A #N/A TRUE FALSE FALSE (lRF-2-binding protein 2} (IRF-2BP2) Smad nuclear-interacting protein 1 (FHA Q8TAD8 SNIP1 396 #N/A #N/A #N/A FALSE FALSE TRUE domain-containing protein SNIP1)

E3 ubiquitsn-protein ligase UHRF1 (EC 2.3.2.27) (Inverted CCAAT box-binding protein of 90 kDa) (Nuclear protein 95) (Nuclear zinc finger protein Np95) (HuNp9S) (hNp95) (RING finger protein 106) (RING-type E3 ubiquitin Q96T88 UHRF1 793 #N/A #N/A #N/A FALSE TRUE TRUE transferase UHRF1) (Transcription factor ICBP90) (Ubiquitin-like PHD and RING finger domain-containing protein 1) (hUHRFI) (Ubiquitin-iike-containing PHD and RING finger domains protein 1)

Protein po!ybromo-1 (hPB1) (BRG1- Q86U86 PBR 1 associated factor 180) (BAF18Q) (Polybromo- 1689 #N/A #N/A #N/A FALSE FALSE TRUE 1D) Peroxisomal membrane protein PEX14 (PTS1 receptor-docking protein) (Peroxin-14) 075381 PEX14 377 #N/A #N/A #N/A FALSE. FALSE (Peroxisomal membrane anchor protein PEX14) Peptidyi-prolyl cis-trans isornerase FKBP1A (PPiase FKBP1A) (EC 5.2.1 .8) (12 kDa FK506-binding protein) (12 kDa FKBP) (FKBP- P62942 FKBP1A 108 #N/A #N/A #N/A TRUE FALSE FALSE 12) (Calstabin-1) (FK506-binding protein 1A) (FKBP-1A) (Immunophiiin FKBP12) (Rotamase) Septin-1 (LARP) (Peanut-like protein 3) Q8WYJ6 42979 (Serologically defined breast cancer antigen 367 #N/A #N/A #N/A FALSE FALSE FALSE NY-BR-24) Mitochondrial 2-oxoglutarate/malate carrier Q02978 protein (OGCP) (Solute carrier family 25 314 #N/A #N/A #N/A TRUE TRUE TRUE member 11) Aldose reductase (AR) (EC 1. 1 . 1 2 1) Ρ15121 AKR1 B 1 (Aldehyde reductase) (Aldo-keto reductase 316 #N/A #N/A #N/A TRUE TRUE TRUE family 1 member B1) Q9H6D7 HAUS4 HAUS augmin-like complex subunit 4 363 #N/A #N/A #N/A FALSE FALSE FALSE Myotubularin-related protein 5 (SET-binding 095248 SBF1 1867 #N/A #N/A #N/A FALSE FALSE FALSE factor 1) (Sbf1) 06071 1 LPXN Leupaxin 386 #N/A #N/A #N/A FALSE FALSE TRUE Centrosomal protein of 4 1 kDa (Cep41) Q9BYV8 CEP41 373 #N/A #N/A #N/A FALSE FALSE FALSE (Testis-specific gene A 1 protein) Folylpolyg!utamate synthase, mitochondrial (EC 6.3.2.17) (Folylpoly-gamma-glutamate QQ5932 FPGS synthetase) (FPGS) 587 #N/A #N/A #N/A FALSE FALSE FALSE (Tetrahydrofolylpolyglutamate synthase) (Tetrahydrofolate synthase) Calcium/calmodulin-dependent protein kinase Q16566 CA K4 type IV (Ca V) (EC 2.7.1 1.17) (Ca 473 #N/A #N/A #N/A TRUE TRUE FALSE kinase-GR) Tyrosine-protein phosphatase non-receptor type 7 (EC 3.1 .3.48) (Hematopoietic protein- Ρ35236 ΡΤΡΝ7 360 #N/A #N/A #N/A FALSE FALSE FALSE tyrosine phosphatase) (HEPTP) (Protein- tyrosine phosphatase LC-PTP) DNA polymerase alpha subunit B (DNA Q14181 POLA2 598 #N/A #N/A #N/A FA S . FALSE FALSE polymerase alpha 70 kDa subunit) 075362 ZNF217 Zinc finger protein 217 1048 #N/A #N/A #N/A FALSE FALSE FALSE Rho guanine nucleotide exchange factor 6 EF (Alpha-Pix) (COOL-2) (PAK-interacting Q15052 776 #N/A #N/A #N/A FALSE FALSE FALSE exchange factor alpha) (Rac/Cdc42 guanine nucleotide exchange factor 6)

Tetraspanin-7 (Tspan-7) (Cell surface glycoprotein A15) (Membrane component chromosome X surface marker 1) (T-cell P41732 TSPAN7 249 #N/A #N/A #N/A FALSE TRUE FALSE acute lymphoblastic leukemia-associated antigen 1) (TALLA-1) (Transmembrane 4 superfamily member 2) (CD antigen CD231) Collagen type IV alpha-3-binding protein (Ceramide transfer protein) (hCERT) COL4A3B (Goodpasture antigen-binding proiein) (GPBP) Q9Y5P4 624 #N/A #N/A #N/A FALSE TRUE FALSE P (START domain-containing protein 11) (StARD1 1) (StAR-related lipid transfer protein 11) Testis-specific Y-encoded-like protein 5 Q86VY4 TSPYL5 417 #N/A #N/A #N/A FALSE FALSE FALSE (TSPY-iike protein 5) lnterleukin-32 (IL-32) (Natural killer cells L32 protein 4) (TLfmor necrosis factor alpha- 234 #N/A #N/A #N/A FALSE FALSE FALSE inducing factor) Caicium/calmodulin-dependent protein kinase Q13557 CAMK2D type subunit delta (CaM kinase II subunit 499 #N/A #N/A #N/A FALSE F F delta) (CaMK-ll subunit delta) (EC 2.7.1 1.17) Wings apart-like proiein homolog (Friend of Q7Z5K2 WAPL EBNA2 protein) (WAPL cohesin release 1190 #N/A #N/A #N/A FALSE FALSE FALSE factor) •J\ FYN-binding protein (Adhesion and degranuiation promoting adaptor protein) 0151 17 FYB (ADAP) (FYB-120/130) (p120/p130) (FYN-T- 783 #N/A #N/A #N/A FALSE FALSE FALSE binding protein) (SLAP-130) (SLP-76- associated phosphoprotein) Sulfide:quinone oxidoreductase, mitochondria Q9Y6N5 SQOR (SQOR) (EC 1.8.5.-) (Sulfide quinone 450 #N/A #N/A #N/A TRUE TRUE TRUE oxidoreductase) TTI2 TEL02-interacting protein 2 508 #N/A #N/A #N/A FALSE FALSE FALSE

Q9NV 6 DNAJC17 DnaJ homolog subfamily C member 17 304 #N/A #N/A #N/A TRUE FALSE FALSE Nck-associated protein 1-like (Hematopoietic P55160 NCKAP1 L protein 1) (Membrane-associated protein HE 1127 #N/A #N/A #N/A TRUE FALSE FALSE 1) Q08AF3 SLFN5 Schlafen family member 5 891 #N/A #N/A #N/A FALSE FALSE FALSE Serine/threonine-protein phosphatase 6 Q9UPN7 PPP6R1 regulatory subunit 1 (SAPS domain family 881 #N/A #N/A #N/A FALSE FALSE FALS member 1) Glutarninase kidney isoforrn, mitochondrial 094925 GLS (GLS) (EC 3.5.1 .2) (K-glutaminase) (L- 669 #N/A #N/A #N/A FALSE FALSE FALSE glutamine amidohydrolase)

Protein SETSIP (SET pseudogene protein 18) PODMEO SETS1P (SET similar protein) (Similar to SET 302 #N/A #N/A #N/A TRUE FALSE FALSE translocation protein)

CUGBP Elav-iike family member 2 (CELF-2) (Bruno-like protein 3) (CUG triplet repeat RNA- binding protein 2) (CUG-BP2) (CUG-BP- and 095319 CELF2 ETR-3-like factor 2) (ELAV-type RNA-binding 5 8 #N/A #N/A #N/A FALSE FALSE FALSE protein 3) (ETR-3) (Neuroblastoma apoptosis- related RNA-binding protein) (hNAPOR) (RNA- binding protein BRUNOL-3)

Ubiquitin-60S ribosomal protein L40 (CEP52) (Ubiquitin A-52 residue ribosomal protein Ρ62987 UBA52 fusion product 1) [Cleaved into: Ubiquitin; 60S 128 #N/A #N/A #N/A FALSE FALSE FALSE ribosomal protein L40 (Large ribosomal subunit protein eL40)]

Putative methy!transferase C9orf1 14 (EC 2.1 . 1 .-) (Centromere protein 32) (CENP-32) Q5T280 SPOUT1 376 #N/A #N/A #N/A FALSE FALSE FALSE (Kinetochore-associated protein) (SPOUT domain-containing methyltransferase 1)

Succinate-sernia!dehyde dehydrogenase, mitochondrial (EC 1.2.1 .24) (Aldehyde P51649 ALDH5A1 dehydrogenase family 5 member A1) (NAD(+)- 535 #N/A #N/A #N/A FALSE FALSE FALSE dependent succinic semialdehyde dehydrogenase) Integrin aipha-4 (CD49 antigen-like family P13612 ITGA4 member D) (Integrin aipha-IV) (VLA-4 subunit 1032 #N/A #N/A #N/A FALSE FALSE FALSE alpha) (CD antigen CD49d) Cation-independent mannose-6-phosphate receptor (C IV3an-8-P receptor) (CI-MPR) (M6PR) (300 kDa mannose 6-phosphate P 1 17 7 IGF2R receptor) ( PR 300) (Insulin-like growth factor 2491 #N/A #N/A #N/A TRUE TRUE TRUE 2 receptor) ( Insulin-like growth factor II receptor) (IGF-I I receptor) (M6P/IGF2 receptor) (M6P/IGF2R) (CD antigen CD222)

Ribonuclease H2 subunit A (RNase H2 subunit A) (EC 3 .1.26.4) (Aicardi-Goutieres RNASEH Q75792 syndrome 4 protein) (AGS4) (RNase H(35)) 299 #N/A #N/A #N/A FALSE FALSE FALSE 2A (Ribonuclease HI large subunit) (RNase H I large subunit) (Ribonuclease H I subunit A)

Protein phosphatase 1 regulatory subunit 7 Q 5435 PPP1 R7 360 #N/A #N/A #N/A FALSE FALSE FALSE (Protein phosphatase 1 regulatory subunit 22)

GTPase A P family member 5 ( Immunity- associated nucleotide 4-like 1 protein) Q96F1 5 G HAP5 ( mmunity-associated nucleotide 5 protein) 307 #N/A #N/A #N/A FALSE FALSE FALSE (IAN-5) (hlAN5) (immunity-associated protein 3)

Protein LS 14 homoiog B (Protein FA 6 1B) Q9BX40 LSM 14B 385 #N/A #N/A #N/A FALSE FALSE FALSE (RNA-associated protein 55B) (hRAP55B)

Epididymal secretory protein E 1 (Human P61 9 16 NPC2 epididymis-specific protein 1) (He1 ) (Niemann- 15 1 #N/A #N/A #N/A FALSE FALSE FALSE Pick disease type C2 protein) Poly [ADP-ribose] polymerase (PARP-1 0) PARP1 0 (EC 2.4.2.30) (ADP-ribosyitransferase 1025 #N/A #N/A #N/A FALSE FALSE FALSE diphtheria toxin-like 10) (ARTD1 0) DNA repair protein XRCC1 (X-ray repair cross- P 18887 XRCC1 633 #N/A #N/A #N/A TRUE TRUE TRUE complementing protein 1) Q9NP72 Ras-related protein Rab-1 8 2 6 #N/A #N/A #N/A TRUE TRUE TRUE Regulaiion of nuclear pre-mRNA domain containing protein 1A (Cyclin-dependent Q96P16 312 #N/A #N/A #N/A FALSE FALSE FALSE kinase inhibitor 2B-related protein) (p15 related protein)

Ρ35754 GLRX Giutaredoxin-1 (Thioltransferase-1) (TTase-1) 6 #N/A #N/A #N/A TRUE FALSE FALSE Putative ribosome-binding factor A , Q8N0V3 RBFA 343 #N/A #N/A #N/A FALSE FALSE FALSE mitochondrial Dynactin subunit 4 (Dyn4) (Dynactin subunit Q9UJW0 DCTN4 460 #N/A #N/A #N/A TRUE FALSE FALSE p62)

Inositol 1,4,5-trisphosphate receptor type 2 ( PS receptor isoform 2) (1P3R 2) (lnsP3R2) Q14571 ITPR2 2701 #N/A #N/A #N/A FALSE TRUE FALSE (Type 2 inositol 1,4,5-trisphosphate receptor) (Type 2 sP receptor)

cAMP-dependent protein kinase catalytic P22694 PRKACB 351 #N/A #N/A #N/A FALSE FALSE TRUE subunit beta (PKA C-beta) (EC 2.7.1 1. 1 1)

-4 E3 ubiqLfitin-protein ligase TRIP12 (EC 2.3.2.26) (E3 ubiquitin-protein ligase for Arf) Q14669 TRIP12 (ULF) (HECT-type E3 ubiquitin transferase 1992 #N/A #N/A #N/A FALSE FALSE FALSE TRIP12) (Thyroid receptor-interacting protein 12) (TR-interacting protein 12) (TRIP-12)

Beta-adrenergic receptor kinase 1 (Beta-ARK- Ρ25098 GRK2 1) (EC 2.7.1 1.15) (G-protein coupled receptor 689 #N/A #N/A #N/A FALSE FALSE FALSE kinase 2) Deriin-2 (Degradation in endoplasmic Q9GZP9 DERL2 reticulum protein 2) (DERtrin-2) (Der1-like 239 #N/A #N/A #N/A FALSE TRUE FALSE protein 2) (F-LAN-1) (F-LANa) Protein-tyrosine kinase 2-beia (EC 2.7.10.2) (Ca!cium-dependeni tyrosine kinase) (CADTK) (Calcium-regulated non-receptor proline-rich tyrosine kinase) (Cell adhesion kinase beta) Q14289 ΡΤΚ2Β 1009 #N/A #N/A #N/A FALSE FALSE FALSE (CAK-beta) (CAKB) (Focal adhesion kinase 2) (FADK 2) (Proline-rich tyrosine kinase 2) (Related adhesion focal tyrosine kinase) (RAFTK) SH2 domain-containing protein 2A (SH2 domain-containing adapter protein) (T cell- Q9NP31 SH2D2A 389 #N/A #N/A #N/A FALSE FALSE FALSE specific adapter protein) (TSAd) (VEGF receptor-associated protein) Lys-63-specific deubiquitinase BRCC36 (EC 3.4.19.-) (BRCA1-A complex subunit BRCC36) (BRCA1/BRCA2-containing complex P46736 BRCC3 316 #N/A #N/A #N/A F LS Ε F L Ξ F LS EE subunit 3) (BRCA1/BRCA2-containing complex subunit 36) (BRISC complex subunit BRCC36)

Actin-related protein 2/3 complex subunit 2 015144 ARPC2 300 #N/A #N/A #N/A TRUE TRUE TRUE (Arp2/3 complex 34 kDa subunit) (p34-ARC) DNA-binding protein SATB1 (Special AT~rich Q01826 SATB1 763 #N/A #N/A #N/A FALSE FALSE FALSE sequence-binding protein 1) Q9UMY4 SNX12 Sorting nexin-12 172 #N/A #N/A #N/A FALSE FALSE FALSE

Inorganic pyrophosphatase 2 , mitochondrial (EC 3.6.1 .1) (Pyrophosphatase SID6-306) Q9H2U2 ΡΡΑ 2 334 #N/A #N/A #N/A FALSE FALSE FALSE (Pyrophosphate phospho-hydrolase 2) iPPase 2)

Fatty acid desaturase 2 (EC 1 14.19.3) (Acyl- CoA 6-desaturase) (Delta(6) fatty acid 0 9586 FADS2 444 #N/A #N/A #N/A FALSE FALSE FALSE desaturase) (D6D) (Delta(6) desaturase) (Delta-6 desaturase) Melanoma-associated antigen D 1 (MAGE tumor antigen CCF) (MAGE-D1 antigen) Q9Y5V3 778 #N/A #N/A #N/A FALSE FALSE FALSE (Neurotrophin receptor-interacting MAGE homo!og)

P49366 DHPS Deoxyhypusine synthase (DHS) (EC 2.5.1 46) 369 #N/A #N/A #N/A TRUE FALSE TRUE DNA repair protein XRCC4 (X-ray repair cross- Q13426 XRCC4 336 #N/A #N/A #N/A FALSE FALSE FALSE compiementing protein 4) Serine/threonine-protein kinase Chk1 (EC 2.7.1 1.1) (CHK1 checkpoint homoiog) (Cell 0 14757 CHEK1 476 #N/A #N/A #N/A FALSE FALSE FALSE cycle checkpoint kinase) (Checkpoint kinase- 1) EKC/KEOPS complex subunit LAGE3 (L Q14657 LAGE3 antigen family member 3) (Protein ESO-3) 143 # /A #N/A #N/A FALSE FALSE FALSE (Protein ITBA2) Transcription initiation factor MB (General GTF2B 316 #N/A #N/A #N/A F LS Ε F L Ξ F LS EE transcription factor TFI IB) (S300-II) Katanin p60 ATPase-containing subunit A 1 o 075449 KATNA1 (Katanin p6Q subunit A1) (EC 3.6.4.3) (p60 491 #N/A #N/A #N/A FALSE FALSE FALSE katanin) Proteasome subunit beta type- 10 (EC 3.4.25.1) (Low molecular mass protein 10) (Macropain subunit MECI-1) (Muiticatalytic P40306 PSMB10 273 #N/A #N/A #N/A FALSE FALSE FALSE endopeptidase complex subunit MECI-1) (Proteasome MECI-1) (Proteasome subunit beta-2i) WW domain-containing adapter protein with Q9BTA9 WAC 647 #N/A #N/A #N/A FALSE FALSE FALSE coiled-coil Polypeptide N- acetylgalactosaminyltransferase 2 (EC 2.4.1 4 1) (Polypeptide GalNAc transferase 2) (GaiNAc-T2) (pp-GaNTase 2) (Protein-UDP acetylga!actosaminyltransferase 2) (UDP- Q10471 GALNT2 571 #N/A #N/A #N/A TRUE TRUE FALSE GalNAc:po!ypeptide N- acetylgalactosaminyltransferase 2) [Cleaved into: Polypeptide N- acetylgalactosaminyltransferase 2 soluble form] Helicase-like transcription factor (EC 2.3.2.27) (EC 3.6.4.-) (DNA-binding protein/plasminogen activator inhibitor 1 regulator) (HIP1 16) (R NG finger protein 80) Q14527 HLTF (RING-type E3 ubiquitin transferase HLTF) 1009 #N/A #N/A #N/A FALSE FALSE FALSE (SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily A member 3) (Sucrose nonfermenting protein 2 like 3) Unconventional myosin-ib (MYH-1c) (Myosin 043795 Y0 1B 1136 #N/A #N/A #N/A FALSE F FALSE alpha) (MMI-alpha) (MMIa) Vacuolar protein sorting-associated protein 53 Q5VIR6 VPS53 699 #N/A #N/A #N/A FALSE FALSE FALSE homolog Mitogen-activated protein kinase 3 (MAP kinase 3) (MAPK 3) (EC 2.7. 11.24) (ERT2) (Extracellular signal-regulated kinase 1) (ERK- P27361 IA PK3 379 #N/A #N/A #N/A FALSE TRUE FALSE 1) (Insulin-stimulated MAP2 kinase) (MAP kinase isoform p44) (p44-MAPK) (Microtubule- associated protein 2 kinase) (p44-ERK1) Caspase-8 (CASP-8) (EC 3.4.22.61) (Apoptotic cysteine protease) (Apoptotic protease Mch~5) (CAP4) (FADD-homoiogous ICE/ced-3-like protease) (FADD-like ICE) Q14790 CASP8 479 #N/A #N/A #N/A FALSE FALSE FALSE (FLICE) (iCE-iike apoptotic protease 5) ( ORT 1-associated ced-3 homolog) (MACH) [Cleaved into: Caspase-8 subunit p18; Caspase-8 subunit p10]

P14921 ETS1 Protein C-ets-1 (p54) 441 #N/A #N/A #N/A FALSE TRUE TRUE DNA replication complex GINS protein PSF1 Q14691 GINS1 196 #N/A #N/A #N/A FALSE FALSE TRUE (GINS complex subunit 1) Q8WUD1 RAB2B Ras-related protein Rab-2B 216 #N/A #N/A #N/A TRUE TRUE TRUE Fructose-2,6-bisphospbatase TIGAR (EC 3.1 .3.46) (TP53-induced glycolysis and Q9NQ88 TIGAR 270 #N/A #N/A #N/A F FALSE FA apoptosis regulator) (TP53-induced glycolysis regulatory phosphatase) ATP-dependent RNA helicase DHX8 (EC Q 14562 DHX8 3.6.4.13) (DEAH box protein 8) (RNA helicase 1220 #N/A #N/A #N/A FALSE FALSE FALSE HRH1) Nuclear factor NF-kappa-B p105 subunit (DNA- binding factor KBF1) (EBP-1) (Nuclear factor P19838 NFKB1 of kappa light polypeptide gene enhancer in B- 968 #N/A #N/A #N/A FALSE FALSE TRUE cells 1) [Cleaved into: Nuclear factor NF- kappa-B p50 subunit] Transformation/transcription domain- associated protein (350/400 kDa PCAF- Q9Y4A5 TRRAP 3859 #N/A #N/A #N/A FALSE FALSE FALSE associated factor) (PAF350/400) (STAF40) (Tra1 homolog) Acyl-CoA synthetase family member 3 , Q4G176 ACSF3 576 #N/A #N/A #N/A FALSE FALSE FALSE mitochondrial (EC 6.2.1 .-) Serine/threonine-proiein kinase 4 (EC 2.7.1 1.1) (Mammalian STE20~iike protein kinase 1) (MST-1) (STE20-like kinase MST1) Q13043 STK4 (Serine/threonine-protein kinase Krs-2) 487 #N/A #N/A #N/A FALSE FALSE FALSE [Cleaved into: Serine/threonine-protein kinase 4 37kDa subunit (MST1/N); Serine/threonine- protein kinase 4 18kDa subunit (MST1/C)]

SAFB-like transcription modulator (Modulator Q9NWH9 SLTA 1034 #N/A #N/A #N/A TRUE TRUE TRUE of estrogen-induced transcription)

E3 ubiquitin-protein ligase RING1 (EC 2.3.2.27) (Polycomb complex protein RING1) QQ6587 RING1 (RING finger protein 1) (RING-type E3 406 #N/A #N/A #N/A TRUE FALSE TRUE ubiquitin transferase RING1) (Really interesting new gene 1 protein) „ „ GRAM domain-containing protein 4 (Death- Q6IC98 GRAMD4 . . . . . 578 #N/A #N/A #N/A FALSE FALSE FALSE » ndu ng protein)

Nesprin-1 (Enaptin) (KASH domain-containing protein 1) (KASH1) (Myocyte nuclear envelope Q8NF91 SYNE1 protein 1) (Myne-1) (Nuclear envelope spectrin 8797 #N/A #N/A #N/A FALSE FALSE FALSE repeat protein 1) (Synaptic nuclear envelope protein 1) (Syne-1) Protein canopy homolog 3 (CTG repeat protein 4a) (Expanded repeat-domain protein Q9BT09 CNPY3 CAG/CTG 5) (Protein associated with TLR4) 278 #N/A #N/A #N/A FALSE FALSE FALSE (Trinucleotide repeat-containing gene 5 protein) Protein THEMIS (Thymocyte-expressed Q8N1 K5 THEMIS 641 #N/A #N/A #N/A TRUE FALSE FALSE molecule involved in selection) Gasdermin-D (Gasdermin domain-containing protein 1) [Cleaved into: Gasdermin-D, N- P57764 GSDMD 484 #N/A #N/A #N/A FALSE FALSE TRUE terminal (GSDMD-NT); Gasdermin-D, C- terminal (GSDMD-CT)] Runt-relaied transcription factor 1 (Acute myeloid leukemia 1 protein) (Core-binding factor subunit aipha~2) (CBF-alpha~2) (Oncogene AML-1) (Polyomavirus enhancer- Q01 196 RUNX1 453 #N/A #N/A #N/A FALSE FALSE FALSE binding protein 2 alpha B subunii) (PEA2- alpha B) (PEBP2-alpha B) (SL3-3 enhancer factor 1 alpha B subunit) (SL3/AKV core- binding factor alpha B subunit)

Retinoblastoma-binding protein 5 (RBBP-5) Q15291 RBBP5 538 #N/A #N/A #N/A FALSE FALSE FALSE (Retinoblastoma-binding protein RBQ-3) Triokinase/FMN cyclase (Bifunctional ATP- dependent dihydroxyacetone kinase/FAD- AMP lyase (cyclizing)) [Includes: ATP- dependent dihydroxyacetone kinase (DHA Q3LXA3 TKFC kinase) (EC 2.7. 1.28) (EC 2.7. 1.29) 575 #N/A #N/A #N/A TRUE FALSE FALSE (Glycerone kinase) (Triokinase) (Triose kinase); FAD-AMP lyase (cyclizing) (EC 4.6.1 .15) (FAD-AMP lyase (cyclic FMN forming)) (FMN cyclase)] E3 ubiquitin-protein ligase BRE1A (BRE1-A) (hBRE1) (EC 2.3.2.27) (RING finger protein Q5VTR2 RNF20 975 #N/A #N/A #N/A TRUE FALSE FALSE 20) (R G-type E3 ubiquitin transferase BRE1A) Sodium/potassium-transporting ATPase subunit alpha-3 (Na(+)/K(+) ATPase alpha-3 P13637 ATP 1A3 subunit) (EC 3.6.3.9) (Na(+)/K(+) ATPase 1013 #N/A #N/A #N/A FALSE FALSE FALSE alpha(lll) subunii) (Sodium pump subunit alpha-3) Heat shock 70 kDa protein 6 (Heat shock 70 P17066 HSPA6 643 #N/A #N/A #N/A FALSE FALSE FALSE kDa protein B') Nischarin (Imidazoline receptor 1) ( - 1) (IR1) (!midazoiine receptor antisera-seiected protein) (hlRAS) (Imidazoline- receptor) (MR) Q9Y N!SCH 1504 #N/A #N/A #N/A FALSE FALSE FALSE (Imidazoline- 1 receptor candidate protein) ( - 1 receptor candidate protein) ( R candidate protein) Myosin light polypeptide 6 (17 Da myosin light chain) (LC17) (Myosin light chain 3) (MLC- P60660 YL6 3) (Myosin light chain alkali 3) (Myosin light 151 #N/A #N/A #N/A FALSE FALSE FALSE chain A3) (Smooth muscle and nonmuscle myosin light chain alkali 6) Charged multivesicular body protein 7 Q8WUX9 CHMP7 453 #N/A #N/A #N/A FALSE FALSE FALSE (Chromatin-modifying protein 7) Syntenin-1 (Melanoma differentiation- associated protein 9) (MDA-9) (Pro-TGF-alpha OQ0560 SDCBP cytoplasmic domain-interacting protein 18) 298 #N/A #N/A #N/A FALSE FALSE FALSE (TAG P18) (Scaffold protein Pbp1) (Syndecan- binding protein 1) Tyrosine-protein phosphatase non-receptor type 6 (EC 3.1 .3.48) (Hematopoietic cell P29350 PTPN6 protein-tyrosine phosphatase) (Protein- 595 #N/A #N/A #N/A FALSE FALSE FALSE tyrosine phosphatase 1C) (PTP-1C) (Protein- tyrosine phosphatase SHP-1) (SH-PTP1)

Sterol O-acyltransferase 1 (EC 2.3.1.26) (Acyl- P35610 SOAT1 coenzyme A:cholesterol acyltransferase 1) 550 #N/A #N/A #N/A FALSE FALSE FALSE (ACAT-1) (Cholesterol acyltransferase 1)

Q9BRJ6 C7orf50 Uncharacterized protein C7orf50 194 #N/A #N/A #N/A FALSE FALSE FALSE Q92608 DOC 2 Dedicator of cytokinesis protein 2 1830 #N/A #N/A #N/A FALSE FALSE FALSE LanC-like protein 1 (40 kDa erythrocyte 043813 LANCL1 399 #N/A #N/A #N/A FALSE FALSE FALSE membrane protein) (p40)

DNA ligase 4 (EC 6.5.1 .1) (DNA ligase V) P49917 LIG4 9 11 #N/A #N/A #N/A FALSE FALSE FALSE (Polydeoxyribonucleotide synthase [ATP] 4) Fatiy aldehyde dehydrogenase (EC 1.2 1.3) (Aldehyde dehydrogenase 10) (Aldehyde Ρ51648 ALDH3A2 485 #N/A #N/A #N/A FALSE FALSE FALSE dehydrogenase family 3 member A2) (Microsomal aldehyde dehydrogenase)

Q14019 COTL1 Coaciosin-like protein 142 #N/A #N/A #N/A FALSE FALSE FALSE Structural maintenance of chromosomes Q8IY18 S C5 1101 #N/A #N/A #N/A FALSE FALSE FALSE protein 5 (SMC protein 5) (SMC-5) (hSMC5)

Transcriptional repressor protein YY1 (Delta Ρ25490 ΥΥ1 transcription factor) ( O80 complex subunit 414 #N/A #N/A #N/A TRUE TRUE FALSE S) (NF-E1) (Yin and yang 1) (YY-1) Cytoskeleton-associated protein 2 (CTCL Q8WWK9 CKAP2 tumor antigen se20-10) (Tumor- and 683 #N/A #N/A #N/A FALSE FALSE FALSE microtubuie-associated protein) Ρ32121 ARRB2 Beta-arrestin-2 (Arrestin beta-2) 409 #N/A #N/A #N/A FALSE FALSE TRUE ZC3HAV1 Q96H79 Zinc finger CCCH-type antiviral protein 1-like 300 #N/A #N/A #N/A FALSE FALSE FALSE L Alpha-1 ,2-mannosyltransferase ALG9 (EC 2.4.1 .259) (EC 2.4.1 .261) (Asparagine-iinked glycosylation protein 9 homolog) (Disrupted in bipolar disorder protein 1) (Dol-P- Q9H6U8 ALG9 6 1 #N/A #N/A #N/A FALSE FALSE FALSE Man:Man(6)GicNAc(2)-PP-Doi alpha- 1,2- mannosyltransferase) (Dol-P- Man:Man(8)GlcNAc(2)-PP-Dol aipha-1 ,2- mannosyltransferase) Testis-expressed protein 264 (Putative TEX264 313 #N/A #N/A #N/A FALSE FALSE FALSE secreted protein Zsigl 1)

E3 ubiquitin-protein ligase RNF213 (EC 2.3.2.27) (EC 3.6.4 -) (ALK lymphoma Q63HN8 RNF213 oligomerization partner on chromosome 17) 5207 #N/A #N/A #N/A FALSE FALSE TRUE (Mysterin) (R G finger protein 213) (RING- type E3 ubiquitin transferase RNF213) STE20/SPS1 -related proline-alanine-rich protein kinase (Ste-20-related kinase) (EC Q9UEW8 STK39 545 #N/A #N/A #N/A TRUE FALSE TRUE 2.7.1 1 1) (DCHT) (Serine/threonine-protein kinase 39) TBC1 D5 TBC1 domain family member 5 795 #N/A #N/A #N/A FALSE FALSE TRUE Acyl-CoA synthetase family member 2 , Q96C 8 ACSF2 615 #N/A #N/A #N/A FALSE FALSE FALSE mitochondrial (EC 6.2.1 .-)

Dehydrogenase/reductase SDR family member 4 (EC 1. 1 . 1 .184) (NADPH-dependent carbonyl reductase/NADP-retinol dehydrogenase) (CR) (PHCR) (NADPH- dependent retinoi dehydrogenase/reductase) Q9BTZ2 DHRS4 278 #N/A #N/A #N/A TRUE FALSE FALSE (NRDR) (humNRDR) (Peroxisomal short-chain alcohol dehydrogenase) (PSCD) (SCAD-SRL) (Short chain dehydrogenase/reductase family 25C member 2) (Short-chain dehydrogenase/reductase family member 4)

Histidine triad nucleotide-binding protein 2 , Q9BX68 HINT2 mitochondrial (HINT-2) (EC 3.-.-.-) (HINT-3) 163 #N/A #N/A #N/A TRUE FALSE TRUE (H!T-17kDa) (PKCi-1 -related HIT protein)

Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) (lnterleukin-2-inducibie T-ceil kinase) QQ8881 TK (IL-2-inducible T-celi kinase) (Kinase E T) (T- 620 #N/A #N/A #N/A FALSE FALSE FALSE cell-specific kinase) (Tyrosine-protein kinase Lyk) Anoctamin-6 (Small-conductance calcium- Q4KMQ2 AN06 activated nonselective cation channel) (SCAN 910 #N/A #N/A #N/A FALSE FALSE FALSE channel) (Transmembrane protein 16F) E3 ubiquitin-proiein ligase Praja~2 (Praja2) 043164 PJA2 (EC 2.3 2.27) (RING finger protein 131) (RING- 708 #N/A #N/A #N/A FALSE FALSE FALSE type E3 ubiqLfitin transferase Praja-2)

Q9HB07 C12orf10 UPF0160 protein MYG1 , mitochondrial 376 #N/A #N/A #N/A FALSE FALSE FALSE ATPase WRNIP1 (EC 3.6.1 .3) (Werner Q96S55 WRNIP1 665 #N/A #N/A #N/A FALSE TRUE FALSE helicase-interacting protein 1) P15498 VAV1 Proto-oncogene vav 845 #N/A #N/A #N/A FALSE FALSE FALSE QQ6945 SOX4 Transcription factor SOX-4 474 #N/A #N/A #N/A FALSE FALSE FALSE Activity-dependent neuroprotector homeobox Q9H2P0 ADNP protein (Activity-dependent neuroprotective 1102 #N/A #N/A #N/A FALSE TRUE FALSE protein)

Transcription factor 12 (TCF-12) (Class B basic helix-loop-heiix protein 20) (bHLHb20) Q99081 TCF12 682 #N/A #N/A #N/A FALSE FALSE FALSE (DNA-binding protein HTF4) (E-box-binding protein) (Transcription factor HTF-4)

* Q15283 RASA2 s ^TPase-activating protein 2 (GTPase- 850 #N/A #N/A #N/A F FALSE F activating protein 1m) (GAP1m) PATCH Q9UKJ3 G patch domain-containing protein 8 1502 #N/A #N/A #N/A F FALSE FALSE o LDLR chaperone ESD (Mesoderm development candidate 2) (Mesoderm Q14696 MESDC2 234 #N/A #N/A #N/A TRUE FALSE FALSE development protein) (Renal carcinoma antigen NY-REN-61) Tetratricopeptide repeat protein 33 (TPR Q6PID6 TTC33 repeat protein 33) (Osmosis-responsive #N/A #N/A #N/A FALSE FALSE FALSE factor) Ubiquitin-like protein ISG15 (Interferon- induced 15 kDa protein) (interferon-induced P05161 ISG15 165 #N/A #N/A #N/A FALSE TRUE FALSE 17 kDa protein) (IP17) (UbiqLfitin cross- reactive protein) (hUCRP) MRG/MORF4L-binding protein (MRG-bindinc Q9NV56 MRGBP protein) (Up-regulated in colon cancer 4) 204 #N/A #N/A #N/A FALSE TRUE FALSE (Urcc4) Ankyrin repeat and LE domain-containing Q86XL3 ANKLE2 938 #N/A #N/A #N/A FALSE FALSE TRUE protein 2 (LE domain-containing protein 4) Homeobox protein SIX3 (Sine oculis 095343 SIX3 332 #N/A #N/A #N/A FALSE FALSE FALSE homeobox homolog 3) Phosphatidylinositol transfer protein alpha QQ0169 PITPNA isoform (P TP a pha) (Ptdlns transfer protein 270 #N/A #N/A #N/A FALSE TRUE FALSE alpha) (PtdinsTP alpha) Q9NZD2 GLTP Giycolipid transfer protein (GLTP) 209 #N/A #N/A #N/A FALSE FALSE FALSE Mitotic spindle-associated MXD complex Q9Y3D0 FAM96B subunit MIP18 (MSS19-interacting protein of 163 #N/A #N/A #N/A FALSE FALSE TRUE 8 kDa) (Protein FAM96B)

Ubiquitin/ISG15-conjugating enzyme E2 L6 (EC 2.3.2.23) (E2 ubiquitin-conjugating 014933 UBE2L6 enzyme L6) (Retinoic acid-induced gene B 153 #N/A #N/A #N/A FALSE FALSE FALSE protein) (RIG-B) (UbcHS) (Ubiquitin carrier protein L6) (Ubiquitin-protein ligase L6)

Pogo transposabie element with ZNF domain Q7Z3K3 POGZ (Suppressor of hairy wing homolog 5) (Zinc 1410 #N/A #N/A #N/A FALSE FALSE FALSE finger protein 280E) (Zinc finger protein 635) Retinoic acid receptor RXR-aipha (Nuclear Ρ 19793 RXRA receptor subfamily 2 group B member 1) 462 #N/A #N/A #N/A FALSE FALSE FALSE (Retinoid X receptor alpha) Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical] (EC 3.6.1 .17) (Diadenosine 5',5"'-P1 ,P4-tetraphosphate asymmetrical Ρ50583 NUDT2 hydrolase) (Ap4A hydrolase) (Ap4Aase) 147 #N/A #N/A #N/A TRUE FALSE FALSE (Diadenosine tetraphosphatase) (Nucleoside diphosphate-linked moiety X motif 2) (Nudix motif 2)

La-related protein 4 (La ribonucieoprotein Q71RC2 LARP4 724 #N/A #N/A #N/A FALSE FALSE FALSE domain family member 4) Ubiquitin-protein ligase E3A (EC 2.3.2.26) (E6AP ubiquitin-proiein ligase) (HECT-type UBE3A n transferase E3A) (Human Q05086 875 #N/A #N/A #N/A FALSE TRUE FALSE papillomavirus E6-associated protein) (Oncogenic protein-associated protein E6-AP) (Renal carcinoma antigen NY-REN-54)

Ribonuclease H2 subunit B (RNase H2 RNASEH subunit B) (Aicardi-Goutieres syndrome 2 Q5TBB1 312 #N/A #N/A #N/A TRUE FALSE TRUE 2B protein) (AGS2) (Deleted in lymphocytic leukemia 8) (Ribonuclease H I subunit B)

Lysophosphatidylcholine acyltransferase 1 (LPC acyltransferase 1) (LPCAT-1) (LysoPC acyltransferase 1) (EC 2.3.1 .23) (1- acylgiycerophosphocholine O-acyltransferase) (1-aikylglycerophosphochoiine O- acetyltransferase) (EC 2.3.1 .67) (Acetyl- Q8NF37 LPCAT1 534 #N/A #N/A #N/A FALSE FALSE FALSE o CoA:iyso-platelet-activating factor acetyltransferase) (Acetyl-CoA:lyso-PAF acetyltransferase) (Lyso-PAF acetyltransferase) (LysoPAFAT) (Acyltransferase-like 2) (Phosphonoformate immuno-associated protein 3)

Protein NDRG3 (N-myc downstream-regulated Q9UGV2 NDRG3 375 #N/A #N/A #N/A FALSE FALSE FALSE gene 3 protein) Neuropathy target esterase (EC 3.1 . 1 .5) Q8IY17 PNPLA6 (Patatin-like phospholipase domain-containing 1366 #N/A #N/A #N/A FALSE FALSE FALSE protein 6) Ganglioside-induced differentiation-associated Q8TB36 GDAP1 358 #N/A #N/A #N/A FALSE FALSE FALSE protein 1 (GDAP1) GTPase A P family member 4 (Immunity- Q9NUV9 GIMAP4 associated nucleotide 1 protein) (IAN-1) 329 #N/A #N/A #N/A FALSE FALSE TRUE (hlAN1) (Immunity-associated protein 4) UDP-g cose 6-dehydrogenase (UDP-Gic 060701 UGDH dehydrogenase) (UDP-G!cDH) (UDPGDH) 494 #N/A #N/A #N/A FALSE FALSE FALSE (EC 1. 1 . 1 .22) Haloacid dehalogenase-like hydrolase domain- Q9BXW7 HDHD5 containing 5 (Cat eye syndrome critical region 423 #N/A #N/A #N/A TRUE FALSE FALSE protein 5) Dynactin subunit 3 (Dynactin complex subunit 075935 DCTN3 186 #N/A #N/A #N/A FALSE FALSE FALSE 22 kDa subunit) (p22) Q9ULE6 PALD1 Paladin 856 #N/A #N/A #N/A FALSE FALSE FALSE AP-3 complex subunit sigma-1 (AP-3 complex subunit sigma-3A) (Adaptor-related protein complex 3 subunit sigma-1) (Clathrin- Q92572 AP3S1 193 #N/A #N/A #N/A F LS Ε F L Ξ F LS EE associated/assembly/adaptor protein, small 3) (Sigma~3A-adaptin) (SigmaSA-adaptin) (Sigma-adaptin 3a)

Peroxisomal targeting signal 1 receptor (PTS1 receptor) (PTS1 R) (PTS1-BP) (Peroxin-5) P50542 PEX5 639 #N/A #N/A #N/A FALSE FALSE FALSE (Peroxisomal C-terminal targeting signal import receptor) (Peroxisome receptor 1)

Proteasome subunit beta type-8 (EC 3.4.25.1) (Low molecular mass protein 7) (Macropain subunit C13) (Multicataiytic endopeptidase P28062 PSMB8 276 #N/A #N/A #N/A TRUE FALSE FALSE complex subunit C13) (Proteasome component C13) (Proteasome subunit beta-Si) (Really interesting new gene 10 protein)

P35080 PFN2 Profilin-2 (Profiiin II) 140 #N/A #N/A #N/A FALSE FALSE FALSE Pyridoxine-S'-phosphate oxidase (EC 1.4.3.5) Q9NVS9 PNPO 261 #N/A #N/A #N/A FALSE FALSE FALSE (Pyridoxamine-phosphate oxidase) Guanine nucleotide-binding protein P63218 GNG5 68 #N/A #N/A #N/A TRUE FALSE FALSE G(l)/G(S)/G(0) subunit gamma-5 Chromosome transmission fidelity prot Q8WVB6 CHTF18 975 #N/A #N/A #N/A TRUE TRUE FALSE ho o og (hCTF18) (CHL12) DNA replication complex GI S protein PSF3 Q9BRX5 GINS3 216 #N/A #N/A #N/A FALSE FALSE FALSE (G S complex subunit 3)

Q66K14 TBC1 D9B TBC1 domain family member 9B 1250 #N/A #N/A #N/A FALSE FALSE FALSE

A6NHL2 TUBALS Tubulin alpha chain-like 3 446 #N/A #N/A #N/A FALSE FALSE FALSE Phosphomevaionate kinase (PMKase) (hPMK) Q15126 r 192 #N/A #N/A #N/A TRUE TRUE TRUE (EC 2.7.4.2)

Q8WUH6 TMEM263 Transmembrane protein 263 116 #N/A #N/A #N/A FALSE FALSE FALSE

E3 ubiquitin-protein ligase IV1YCBP2 (EC 2.3.2.27) (Myc-binding protein 2) 075592 MYCBP2 (Pam/highwire/rpm-1 protein) (Protein 4640 #N/A #N/A #N/A FALSE TRUE FALSE associated with yc) (RING-type E3 ubiquitin transferase MYCBP2)

Very-long-chain (3R)-3-hydroxyacyi-CoA dehydratase 1 (EC 4.2.1.134) (3-hydroxyacyl- BQYJ81 HACD1 CoA dehydratase 1) (HACD1) (Cementum- 288 #N/A #N/A #N/A F FALSE F attachment protein) (CAP) (Protein-tyrosine phosphatase-iike member A)

Phosphoglucomutase-1 (PGM 1) (EC 5.4.2.2) P36871 PG 1 562 #N/A #N/A #N/A F FALSE FALSE (Glucose phosphomutase 1) Nuclear factor of activated T-cells, cytoplasmic 2 (NF-ATc2) (NFATc2) (NFAT pre-existing Q 13469 NFATC2 925 #N/A #N/A #N/A F FALSE FALSE subunit) (NF~ATp) (T-cell transcription factor NFAT1) Brefeidin A-inhibited guanine nucleofide- exchange protein 2 (Brefeidin A-inhibited GEP Q9Y6D5 ARFGEF2 1785 #N/A #N/A #N/A FALSE FALSE FALSE 2) (ADP-ribosylation factor guanine nucleotide- exchange factor 2) ARF GTPase-activating protein GIT1 (ARF GAP GIT1) (Cool-associated and tyrosine- Q9Y2X7 GIT1 phosphoryiated protein 1) (CAT-1) (CAT1) (G 761 #N/A #N/A #N/A FALSE FALSE FALSE protein-coupled receptor kinase-interacfor 1) (GRK-interacting protein 1) Protein furry homo!og-like (ALL1 -fused gene 094915 FRYL 3013 #N/A #N/A #N/A FALSE FALSE FALSE from chromosome 4p12 protein) Zinc finger MYM-type protein 2 (Fused in myeloproliferative disorders protein) Q9UBW7 Z YM2 1377 #N/A #N/A #N/A FALSE FALSE FALSE (Rearranged in atypical myeloproliferative disorder protein) (Zinc finger protein 198) Protein TASOR (CTCL tumor antigen se89-1) Q9U 61 FAM208A (Retinoblastoma-associated protein RAP14Q) 1670 #N/A #N/A #N/A FALSE FALSE FALSE (Transgene activation suppressor protein)

Q9P107 G P GEM-interacting protein (GMiP) 970 #N/A #N/A #N/A FALSE FALSE FALSE tRNA modification GTPase GTPBP3, Q969Y2 GTPBP3 mitochondrial (GTP-binding protein 3) 492 #N/A #N/A #N/A FALSE TRUE FALSE (Mitochondrial GTP-binding protein 1) Calcium-regulated heat-stable protein 1 CARHSP Q9Y2V2 (Calcium-regulated heat-stable protein of 24 147 #N/A #N/A #N/A FALSE FALSE FALSE 1 kDa) (CRHSP-24) Cytochrome c oxidase assembly protein Q9Y6N1 COX 11 276 #N/A #N/A #N/A FA S . FALSE FALSE COX1 1, mitochondrial Nucieoiysin Τ Α 1 isoform p40 (RNA-binding P31483 TIA1 protein ΤΊ Α-1) (T-ceil-restricted intracellular 386 #N/A #N/A #N/A FALSE FALSE FALSE antigen-1) (TIA-1) (p40-TIA-1) SHC-transforming protein 1 (SHC- transforming protein 3) (SHC-transforming P29353 SHC1 protein A) (Src homology 2 domain-containing- 583 #N/A #N/A #N/A FALSE FALSE FALSE transforming protein C1) (SH2 domain protein C1) Helicase SKI2W (Ski2) (EC 3.6.4 -) (Helicase- Q15477 S IV2L 1246 #N/A #N/A #N/A FALSE FALSE FALSE ike protein) (HLP) DCC-interacting protein 13-alpha (Dip13- Q9UKG1 APPL1 alpha) (Adapter protein containing PH domain, 709 #N/A #N/A #N/A FALSE FALSE FALSE PTB domain and leucine zipper motif 1)

Kinesin light chain 4 (KLC 4) (Kinesin-like Q9NSK0 KLC4 619 #N/A #N/A #N/A FALSE FALSE FALSE protein 8) ATP syntbase-coupling factor 6 , mitochondrial P18859 ATP5J 108 #N/A #N/A #N/A FALSE FALSE FALSE (ATPase subunit F6) 000255 ΕΝ1 Menin 615 #N/A #N/A #N/A FALSE FALSE FALSE TATA box-binding protein-associated factor RNA polymerase i subunit B (RNA polymerase l-specific TBP-associated factor Q53T94 TAF1 B 63 kDa) (TAFI63) (TATA box-binding protein- 588 #N/A #N/A #N/A FALSE FALSE FALSE associated factor 1B) (TBP-associated factor B) (Transcription initiation factor SL1/T F- B subunit B) T-cel! surface glycoprotein CD5 (Lymphocyte Ρ06127 495 #N/A #N/A #N/A FALSE FALSE FALSE antigen T1/Leu-1) (CD antigen CDS) ATP-dependent RNA heiicase DDX3Y (EC 015523 DDX3Y 3.6.4.13) (DEAD box protein 3 , Y- 660 #N/A #N/A #N/A FALSE FALSE FALSE chromosomai) GTPase Era, mitochondrial (H-ERA) (hERA) 075616 ERAL1 (Conserved ERA-!ike GTPase) (CEGA) (ERA- 437 #N/A #N/A #N/A FALSE FALSE FALSE W) (ERA-like protein 1)

E3 ubiquitin-protein ligase MARCH5 (EC 2.3.2.27) (Membrane-associated RING finger protein 5) (Membrane-associated R G-CH Q9NX47 42799 278 #N/A #N/A #N/A FALSE FALSE TRUE protein V) (MARCH-V) (Mitochondrial ubiquitin ligase) (MITOL) (RING finger protein 153) (RING-type E3 ubiquitin transferase MARCH5)

Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PP2A B subunit isoform B'-delta) (PP2A B subunit Q14738 PPP2R5D 602 #N/A #N/A #N/A FALSE TRUE FALSE isoform B56-delta) (PP2A B subunit isoform PR61-deita) (PP2A B subunit isoform R5- delta) Signal transducer and activator of transcription Ρ42226 STAT6 #N/A #N/A #N/A FALSE FALSE FALSE Ρ 1233 RALA #N/A #N/A #N/A FALSE FALSE FALSE TBC1 D 10 Q8IV04 Carabin (TBC1 domain family member 10C) 446 #N/A #N/A #N/A FALSE FALSE FALSE 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1 55) (2-hydroxy-dATP diphosphatase) P36639 NUDT1 (EC 3.6.1 .56) (8-oxo-dGTPase) (Nucleoside 197 #N/A #N/A #N/A FALSE FALSE FALSE diphosphate-linked moiety X motif 1) (Nudix motif 1) . ... . Non-structural maintenance of chromosomes NS CE4 Q9NXX6 - element 4 homolog A (NS4EA) (Non-SMC 385 #N/A #N/A #N/A FALSE FALSE FALSE A element 4 homolog A) RNA-binding protein Musashi homolog 2 Q96DH6 SI2 328 #N/A #N/A #N/A FALSE TRUE FALSE (Musashi-2) W D repeat-containing protein 92 (WD repeat- Q96 X6 WDR92 357 #N/A #N/A #N/A FALSE FALSE FALSE containing protein Monad) Docking protein 2 (Downstream of tyrosine 060496 DOK2 412 #N/A #N/A #N/A FALSE F FAL kinase 2) (p56(dok-2)) Q96ST2 IWS1 Protein IWS1 homolog (IWS1-iike protein) 819 #N/A #N/A #N/A F FALSE FALSE

B-cell lymphoma/leukemia 11B (BCL-1 1B) (B- ce CLL/lymphoma 1 B) (COUP-TF- Q9C0K0 BCL1 1B 894 #N/A #N/A #N/A FALSE TRUE TRUE interacting protein 2) (Radiation-induced tumor suppressor gene 1 protein) (hRitl) Oxysterol-binding protein-related protein 11 Q9BXB4 OSBPL1 1 747 #N/A #N/A #N/A FALSE FALSE FALSE (ORP-1 1) (OSBP-related protein 11) Thioredoxin domain-containing protein 12 (EC 1.8.4.2) (Endoplasmic reticulum resident protein 18) (ER protein 18) (ERp18) 095881 TXNDC12 172 #N/A #N/A #N/A FALSE FALSE TRUE (Endoplasmic reticulum resident protein 19) (ER protein 19) (ERp19) (Thioredoxin-like protein p19) (hTLP19) Tyrosine-protein kinase JAK1 (EC 2.7.10.2) P23458 JAK1 1154 #N/A #N/A #N/A FALSE FALSE TRUE (Janus kinase 1) (JAK-1) Actin-related protein 2/3 complex subunit 5 01551 1 ARPC5 151 #N/A #N/A #N/A FALSE FALSE FALSE (Arp2/3 complex 16 kDa subunit) (p16-ARC) Cell division cycle protein 123 homolog 075794 CDC123 336 #N/A #N/A #N/A FALSE FALSE FALSE (Protein D123) (HT-1080) (PZ32) Q96ME7 ZNF512 Zinc finger protein 512 567 #N/A #N/A #N/A FALSE FALSE FALSE Alpha-ketoglutarate-dependent dioxygenase Q9C0B1 FTO FTO (EC 1.14.1 1.-) (Fat mass and obesity- 505 #N/A #N/A #N/A FALSE FALSE FALSE associated protein) Nuclear receptor coactivator 5 (NCoA-5) Q9HCD5 NCOA5 579 #N/A #N/A #N/A FALSE FALSE FALSE (Coactivator independent of AF-2) (CIA) Pleckstrin homology domain-containing family A member 2 (PH domain-containing family A Q9HB19 PLEKHA2 #N/A #N/A FALSE FALSE FALSE member 2) (Tandem PH domain-containing protein 2) (TAPP-2)

Dehydrogenase/reductase SDR family member 7 (EC 1. 1 .-.-) (Retinal short-chain Q9Y394 DHRS7 dehydrogenase/reductase 4) (retSDR4) (Short 339 #N/A #N/A #N/A TRUE FALSE TRUE chain dehydrogenase/reductase family 34C member 1)

SAM and SH3 domain-containing protein 3 075995 SASH3 (SH3 protein expressed in lymphocytes 380 #N/A #N/A #N/A FALSE FALSE FALSE homolog) T-ce surface glycoprotein CD1c (CD antigen Ρ29017 CD1C 333 #N/A #N/A #N/A FALSE FALSE FALSE CD1c) Macrophage-capping protein (Actin regulatory Ρ40121 CAPG 348 #N/A #N/A #N/A FALSE FALSE FALSE protein CAP-G) Mannose-1 -phosphate guanyltransferase beta (EC 2.7.7.13) (GDP-mannose Q9Y5P6 G PPB 360 #N/A #N/A #N/A FALSE FALSE FALSE pyrophosphorylase B) (GTP-mannose-1- phosphate guanyiyltransferase beta) Formin-binding protein 1 (Formin-binding Q96RU3 FNBP1 617 #N/A #N/A #N/A FALSE FALSE FALSE protein 17) (hFBP17)

Lysosome-associated membrane glycoprotein 1 (LAMP-1) (Lysosome-associated membrane Ρ 1279 LA P1 417 #N/A #N/A #N/A FALSE FALSE FALSE protein 1) (CD107 antigen-like family member A) (CD antigen CD107a) Iniegrin beta-1 (Fibronectin receptor subunit Ρ05556 ITGB1 beta) (Glycoprotein !la) (GP A) (VLA-4 798 #N/A #N/A #N/A FALSE FALSE FALSE subunit beta) (CD antigen CD29) Chromosome-associated kinesin KIF4A 095239 K1F4A 1232 #N/A #N/A #N/A TRUE FALSE TRUE (Chromokinesin-A) 075909 CCNK Cyclin-K 580 #N/A #N/A #N/A FALSE FALSE FALSE Centrosomal protein of 70 kDa (Cep170) Q5SW79 CEP170 (KARP-1-binding protein) (KARP1-binding 1584 #N/A #N/A #N/A FALSE FALSE FALSE protein) T-ce surface glycoprotein CDS delta chain (T- Ρ04234 CD3D ce receptor T3 delta chain) (CD antigen 171 #N/A #N/A #N/A FALSE FALSE FALSE CD3d) Q92930 RAB8B Ras-related protein Rab-8B 207 #N/A #N/A #N/A FALSE FALSE FALSE Survival of motor neuron-related-splicing factor 30 (30 kDa splicing factor SMNrp) (S N- 075940 S NDC1 238 #N/A #N/A #N/A FALSE FALSE FALSE reiated protein) (Survival motor neuron domain- containing protein 1) TIMELES Q9UNS1 Protein timeless homolog (hT S ) 1208 #N/A #N/A #N/A FALSE FALSE FALSE S Double-stranded RNA-binding protein Sfaufen Q9NUL3 STAU2 570 #N/A #N/A #N/A FALSE FALSE FALSE homolog 2 Crooked neck-like protein 1 (Crooked neck Q9BZJ0 CRNKL1 848 #N/A #N/A #N/A TRUE FALSE TRUE homolog) (hCrn) von Willebrand factor A domain-containing Α3Κ Η 1 VWA8 1905 #N/A #N/A #N/A FALSE FALSE FALSE protein 8

Persulfide dioxygenase ETHE1 , mitochondrial (EC 1.13.1 1.18) (Ethylmalonic encephalopathy 095571 ETHE1 254 #N/A #N/A #N/A FALSE FALSE FALSE protein 1) (Hepatoma subtracted clone one protein) (Sulfur dioxygenase ETHE1)

P01850 TRBC1 T-celi receptor beta-1 chain C region 177 #N/A #N/A #N/A TRUE TRUE TRUE Inositol hexakisphosphate and diphosphoinositoi-pentakisphosphate kinase 1 (EC 2.7.4.21) (EC 2.7.4.24) (Diphosphoinositol pentakisphosphate kinase 1) (Histidine acid Q6PFW1 ΡΡΙΡ5Κ1 1433 #N/A #N/A #N/A FALSE FALSE FALSE phosphatase domain-containing protein 2A) ( P5 kinase) (inositol pyrophosphate synthase 1) (insP6 and PP-IP5 kinase 1) (VI P 1 homolog) (hsVIPI)

HLA class I histocompatibility antigen, B-7 Ρ01889 HLA-B 362 #N/A #N/A #N/A FALSE FALSE FALSE alpha chain ( HC class 1antigen B*7)

GDP-mannose 4,6 dehydratase (EC 4.2. 1.47) 060547 G DS 372 #N/A #N/A #N/A FALSE TRUE FALSE (GDP-D-mannose dehydratase) (GMD)

Q86YVQ RASAL3 RAS protein activator like-3 1 11 #N/A #N/A #N/A FALSE TRUE Q8ND24 RNF214 RING finger protein 214 703 #N/A #N/A #N/A FALSE FALSEi FALSE

Q9NXW2 DNAJB12 DnaJ homolog subfamily B member 12 375 #N/A #N/A #N/A FA FALSE FALSE

00 Q76FK4 N L8 Nucleolar protein 8 (Nucleolar protein Nop1 32) 1167 #N/A #N/A #N/A FA LS FALSE FALSE

Bromodomain-containing protein 2 (027.1 .1) P25440 BRD2 801 #N/A #N/A #N/A FALSE FALSE FALSE (Really interesting new gene 3 protein)

Serine/Arginine-related protein 53 (SRrp53) Q96IZ7 RSRC1 334 #N/A #N/A #N/A FALSE FALSE FALSE (Arginine/serine-rich coi ed-coi protein 1)

E3 ubiquitin-protein ligase AMFR (EC 2.3.2.27) (Autocrine motility factor receptor) Q9UKV5 AMFR (AMF receptor) (RING finger protein 45) 643 #N/A #N/A #N/A FALSE FALSE FALSE (R!NG-type E3 ubiquitin transferase AMFR) (gp78)

H7BZ55 CROCC2 Putative ciliary rootlet coiled-coii protein 2 1655 #N/A #N/A #N/A FALSE FALSE FALSE Bifunciional polynucleotide phosphatase/kinase (DNA 5'-kinase/3'~ phosphatase) (Polynucleotide kinase-3'- Q96T60 PNKP phosphatase) [Includes: Polynucleotide 3'- 521 #N/A #N/A #N/A FALSE FALSE FALSE phosphatase (EC 3.1 3.32) (2'(3'}~ polynucleotidase); Polynucleotide 5'-hydroxyl- kinase (EC 2.7.1 .78)] CGG triplet repeat-binding protein 1 (CGG- Q9UFW8 CGGBP1 binding protein 1) (20 kDa CGG-binding 167 #N/A #N/A #N/A FALSE FALSE FALSE protein) (p20-CGGBP DNA-binding protein) 3-ketodihydrosphingosine reductase (KDS reductase) (EC 1.1.1 .102) (3- dehydrosphinganine reductase) (Follicular Q06136 332 #N/A #N/A #N/A FALSE FALSE FALSE variant translocation protein 1) (FVT-1) (Short chain dehydrogenase/reductase family 35C member 1) Trans-acting T-cell-specific transcription factor P23771 GATA3 443 #N/A #N/A #N/A FALSE FALSE FALSE GATA-3 (GATA-binding factor 3)

Q9NQ1 1 ATP13A2 Cation-transporiing ATPase 13A2 (EC 3.6.3.-) 1180 #N/A #N/A #N/A FALSE FALSE FALSE Immunoglobulin superfamily member 8 (IgSFS) (CD81 partner ) (Glu-Trp-lle E i motif-containing protein 2) (EWI-2) Q969P0 IGSF8 (Keratinocytes-associafed transmembrane 613 #N/A #N/A #N/A FALSE FALSE FALSE protein 4) (KCT-4) (LIR-D1) (Prostaglandin regulatory-like protein) (PGRL) (CD antigen CD316) Obscurin (EC 2.7.1 1.1) (Obscurin-RhoGEF) 55VST9 OBSCN (Obscurin-myosin light chain kinase) 7968 #N/A #N/A #N/A FALSE FALSE FALSE (Obscurin-MLCK) Nucleolar and spindle-associated protein 1 59BXS6 NUSAP1 441 #N/A #N/A #N/A FALSE FALSE FALSE (NuSAP) 3-hydroxyisobuiyryl-CoA hydrolase, mitochondria! (EC 3.1.2 4) (3- Q6NVY1 H!BCH 386 #N/A #N/A #N/A FALSE FALSE FALSE hydroxyisobutyryl-coenzyme A hydrolase) (H!B-CoA hydrolase) (HiBYL-CoA-H) Histone chaperone ASF1 B (Anti-si!encing function protein 1 homolog B) (hAsfl) Q9NVP2 ASF1 B #N/A #N/A FALSE FALSE FALSE (hAsflb) (CCG1 -interacting factor A- i) (CIA-II) (hCIA-ll) interferon-induced protein with tetratricopeptide repeats 5 (!F!T-5) (interferon- Q13325 IFIT5 #N/A #N/A N/A FALSE FALSE FALSE induced 58 kDa protein) (Retinoic acid- and interferon-inducible 58 kDa protein) (P58)

Zinc finger protein 384 (CAG repeat protein 1) (CAS-interacting zinc finger protein) (Nuclear Q8TF68 ZNF384 matrix transcription factor 4) (Nuclear matrix 577 #N/A #N/A iA FALSE TRUE FALSE protein 4) (Trinucleotide repeat-containing o gene 1 protein) o

Q96BY6 DOCK10 Dedicator of cytokinesis protein 10 (Zizimin-3) 2186 #N/A #N/A #N/A FALSE FALSE FALSE Breast cancer type 2 susceptibility protein P51587 BRCA2 3418 N/A #N/A #N/A FALSE FALSE FALSE (Fanconi anemia group D 1 protein) Q9Y6Y8 SEC231P SEC23-interacting protein (p125) 1000 N/A #N/A #N/A FALSE FALSE FALSE Hydroxyacylglutathione hydrolase, Q16775 HAGH mitochondrial (EC 3.1.2.6) (Glyoxa!ase II) (G x 308 #N/A #N/A #N/A FALSE FALSE FALSE

DnaJ homolog subfamily C member 3 075165 DNAJC13 (Required for receptor-mediated endocytosis 2243 #N/A #N/A #N/A FALSE FALSE FALSE 8) (RME-8) DNA repair endonuc!ease XPF (EC 3.1.-.-) (DNA excision repair protein ERCC-4) (DNA Q92889 ERCC4 repair protein complementing XP-F cells) 916 #N/A #N/A #N/A FALSE FALSE FALSE (Xeroderma pigmentosum group F- complementing protein) Phosphotriesterase-related proiein (EC 3.1 .-.-) Q96BW5 PTER 349 #N/A #N/A #N/A FALSE FALSE FALSE (Parathion hydro!ase-re!ated protein) (hPHRP)

Syntaxin-binding protein 1 (MUNC18-1) (N- P61764 STXBP1 Se ) (Protein unc-18 homoiog 1) (Unc18-1) 594 #N/A #N/A #N/A FALSE FALSE TRUE (Protein unc-18 homoiog A) (Unc-18A) (p67)

CD82 antigen (C33 antigen) (IA4) (Inducible membrane protein R2) (Metastasis suppressor P27701 CD82 Kangai-1) (Suppressor of tumorigenicity 6 267 #N/A #N/A #N/A F FALSE F protein) (Tetraspanin-27) (Tspan-27) (CD antigen CD82)

Serine/threonine-protein kinase Nek7 (EC Q8TDX7 NEK7 2.7.1 1.1) (Never in mitosis A-reiated kinase 7) 302 #N/A #N/A #N/A TRUE FALSE FALSE (NimA-re!ated protein kinase 7) CapZ-interacting proiein (Protein kinase Q6JBY9 RCSD1 substrate CapZIP) (RCSD domain-containing 416 #N/A #N/A #N/A FALSE FALSE FALSE o protein 1) Ubiquitin carboxyl-terminai hydrolase 47 (EC 3.4.19.12) (Deubiquitinating enzyme 47) Q96K76 USP47 1375 #N/A #N/A #N/A TRUE FALSE FALSE (Ubiquitin thioesterase 47) (Ubiquitin-specific- processing protease 47) StAR-related lipid transfer protein 3 (Metastatic lymph node gene 64 protein) (MLN Q14849 STARD3 445 #N/A #N/A #N/A FALSE FALSE FALSE 64) (Protein CAB1) (START domain- containing protein 3) (StARDS) Q9U 59 DBR1 Lariat debranching enzyme (EC 3.1.-.-) #N/A #N/A #N/A FALSE FALSE FALSE Q9NWY4 HPF1 Histone PARylation factor 1 346 #N/A #N/A #N/A FALSE TRUE FALSE Magnesium-dependent phosphatase 1 (MDP- Q86V88 MDP1 176 #N/A #N/A #N/A FALSE FALSE FALSE 1) (EC 3.1 .3.-) (EC 3.1 .3.48) Maleylacetoacetate isomerase (MAAI) (EC 043708 GSTZ1 5.2.1 .2) (GSTZ1-1) (Glutathione S-transferase 216 #N/A #N/A #N/A F FALSE FALSE zeta 1) (EC 2.5.1 .18) Protein NDRG1 (Differentiation-related gene 1 protein) (DRG-1) (N-myc downstream- regulated gene 1 protein) (Nickel-specific Q92597 NDRG1 394 #N/A #N/A #N/A FALSE FALSE FALSE induction protein Cap43) (Reducing agents and tunicamycin-responsive protein) (RTP) (Rit42) E3 SUMO-protein iigase PIAS1 (EC 6 3.2.-) (DEAD/H box-binding protein 1) (Gu-binding 075925 P!ASI protein) (GBP) (Protein inhibitor of activated 651 #N/A #N/A #N/A TRUE TRUE FALSE STAT protein 1) (RNA helicase il-binding protein)

Rho-associated protein kinase 1 (EC 2.7.1 1.1) (Renal carcinoma antigen NY-REN-35) (Rho- associated, coiied-coii-containing protein Q13464 ROCK1 1354 #N/A #N/A #N/A FALSE FALSE FALSE kinase 1) (Rho-associated, c i ed-coi containing protein kinase ) (ROCK-i) (p160 ROCK-1) (p160ROCK) o E1A-binding protein p400 (EC 3.6.4.-) (CAG repeat protein 32) (Domino homoiog) Q96L91 EP400 (hDomino) (Trinucleotide repeat-containing 3159 #N/A #N/A #N/A TRUE FALSE FALSE gene 12 protein) (p40Q kDa SWI2/SNF2- related protein)

Q96C01 FAM136A Protein FAM136A 138 #N/A #N/A #N/A TRUE FALSE FALSE Tetratricopeptide repeat protein 5 (TPR repeat Q8N0Z6 TTC5 protein 5) (Stress-responsive activator of 440 #N/A #N/A #N/A TRUE FALSE TRUE p300) (Strap) ATPase family AAA domain-containing protein Q6PL18 ATAD2 2 (EC 3.6.1.3) (AAA nuclear coregulator 1390 #N/A #N/A #N/A FALSE FALSE FALSE cancer-associated protein) (ANCCA)

MOB-like protein phocein (2C4D) (Class II m OB1) (Mob1 homoiog 3) ( ob3) (Mps one Q9Y3A3 OB4 225 #N/A #N/A #N/A FALSE FALSE FALSE binder kinase activator-like 3) (Preimplantation prote 3) Cosiars family protein ABRACL (ABRA C- Q9P1 F3 ABRACL 8 1 #N/A #N/A #N/A FALSE FALSE FALSE terminal-like protein) ER membrane protein complex subunit 4 (Cei Q5J8M3 E C4 proliferation-inducing gene 17 protein) 183 #N/A #N/A #N/A FALSE FALSE FALSE (Transmembrane protein 85) ABRAXA BRISC complex subunit Abraxas 2 (Abraxas Q15018 415 #N/A #N/A #N/A FALSE FALSE FALSE S2 brother protein 1) (Protein FAM175B) THO complex subunit 1 (Tho1) (Nuclear Q96FV9 THOC1 657 #N/A #N/A #N/A TRUE FALSE TRUE matrix protein p84) (p84N5) (hTREX84) Vesicle transport protein GOT1 B (Germ cell tumor 2) (Golgi transport 1 homolog B) Q9Y3E0 GOLT1 B 138 #N/A #N/A #N/A FALSE F F (Putative NF-kappa-B-activating protein 470) (hGOTIa)

Glutathione peroxidase 1 (GPx-1) (GSHPx-1) P072Q3 GPX1 203 #N/A #N/A #N/A FALSE FALSE FALSE (EC 1. 1 1.1 .9) (Cellular glutathione peroxidase) o Prolyl 4-hydroxylase subunit alpha-1 (4~PH P13674 P4HA1 alpha-1) (EC 1.14.1 1.2) (Procoilagen-proline,2- 534 #N/A #N/A #N/A FALSE FALSE FALSE oxoglutarate-4-dioxygenase subunit alpha-1)

Mediator of RNA polymerase transcription subunit 23 (Activator-recruited cofactor 130 kDa component) (ARC130) (Cofactor required for Sp1 transcriptional activation subunit 3) Q9ULK4 MED23 (CRSP complex subunit 3) (Mediator complex #N/A #N/A FALSE FALSE FALSE subunit 23) (Protein sur-2 homolog) (hSur-2) (Transcriptional coactivator CRSP130) (Vitamin D3 receptor-interacting protein complex 130 kDa component) (DRIP130)

Q9ULA0 DNPEP Aspartyl aminopeptidase (EC 3.4.1 1.21) 475 #N/A #N/A #N/A FALSE FALSE FALSE Guanyiate-binding protein 5 (EC 3.6.5.-) (GBP- Q96PP8 GBP5 TA antigen) (GTP-binding protein 5) (GBP-5) 586 #N/A #N/A #N/A FALSE FALSE FALSE (Guanine nudeotide-binding protein 5)

A-kinase anchor protein 13 (AKAP-13) (AKAP- Lbc) (Breast cancer nuclear receptor-binding auxiliary protein) (Guanine nucleotide exchange factor Lbc) (Human thyroid- anchoring protein 31) (Lymphoid blast crisis 2813 #N/A #N/A #N/A FALSE FALSE FALSE oncogene) (LBC oncogene) (Non-oncogenic Rho GTPase-specific GTP exchange factor) (Protein kinase A-anchoring protein 13) (PRKA13) (p47) Negative elongation factor C/D (NELF-C/D) Q8IXH7 NELFCD 590 #N/A #N/A #N/A FALSE FALSE TRUE (TH1-like protein) Nucleosome-remodeling factor subunit BPTF o (Bromodomain and PHD finger-containing Q12830 BPTF 3046 #N/A #N/A #N/A FALSE FALSE FALSE transcription factor) (Fetal A z-5 clone 1 protein) (Fetal Alzheimer antigen)

Prothrombin (EC 3.4.21 .5) (Coagulation factor . ,_ II) [Cleaved into: Activation peptide fragment 622 #N/A #N/A #N/A FALSE FALSE FALSE P00734 F2 . n p p d g m 2 . h m b light chain; Thrombin heavy chain] Mitogen-activated protein kinase 9 (MAP kinase 9) (MAPK 9) (EC 2.7.1 1.24) (JNK-55) P45984 MAPK9 (Stress-activated protein kinase 1a) (SAPKIa) 424 #N/A #N/A #N/A FALSE FALSE FALSE (Stress-activated protein kinase JNK2) (c-Jun N-terminai kinase 2) CCR4-NOT transcription complex subunit 9 Q92600 CNOT9 (Cell differentiation protein RQCD1 homoiog) 299 #N/A #N/A #N/A FALSE FALSE FALSE (Rcd-1) Histone-lysine N-rnethyltransferase 2A (Lysine N-methyliransferase 2A) (EC 2.1 .1.43) (ALL- 1) (CXXC-type zinc finger protein 7) (Myeloid/lymphoid or mixed-!ineage leukemia) (Myeloid/lymphoid or mixed-lineage leukemia Q03164 K T2A protein 1) (Trithorax-like protein) (Zinc finger 3969 #N/A #N/A #N/A FALSE FALSE FALSE protein HRX) [Cleaved into: LL cleavage product N320 (N-ferminai cleavage product of 320 kDa) (p320); MLL cleavage product C180 (C-terminai cleavage product of 180 kDa) (P180)] DNA-directed RNA polymerase subunit RPB3 (RNA polymerase II subunit 3) (RNA polymerase II subunit B3) (DNA-directed RNA P19387 POLR2C 275 #N/A #N/A #N/A FALSE FALSE FALSE polymerase II 33 kDa polypeptide) (RPB33) (DNA-directed RNA polymerase II subunit C) o (RPB31) •J\ Fermitin family homoiog 2 (Kindlin-2) (Mitogen- inducible gene 2 protein) (MIG-2) (Pleckstrin Q96AC1 FER T2 680 #N/A #N/A #N/A FALSE FALSE FALSE homology domain-containing family C member 1) (PH domain-containing family C member 1)

Sodium bicarbonate cotransporter 3 (Electroneutral Na/HCO(3) cotransporter) Q9Y6M7 SLC4A7 (Sodium bicarbonate cotransporter 2) (Sodium 1214 #N/A #N/A #N/A FALSE FALSE FALSE bicarbonate cotransporter 2b) (Bicarbonate transporter) (Solute carrier family 4 member 7) Q86VS8 HOOKS Protein Hook homoiog 3 (h-hook3) (hHK3) 718 #N/A #N/A #N/A FALSE FALSE FALSE General transcription factor E subunit 1 (General transcription factor E 56 kDa P29083 GTF2E1 439 #N/A #N/A #N/A FALSE FALSE FALSE subunit) (Transcription initiation factor E subunit alpha) (TFIIE-alpha) RNA polymerase subunit A C~iermina! Q9NP77 SSU72 domain phosphatase SSU72 (CTD 194 #N/A #N/A #N/A FALSE FALSE FALSE phosphatase SSU72) (EC 3.1 3.16) P36404 ARL2 ADP-ribosylation factor-like protein 2 184 #N/A #N/A #N/A FALSE FALSE FALSE Sp1 0 nuclear body protein (Interferon- Q9HB58 SP1 10 induced protein 41/75) (Speckled 110 kDa) 689 #N/A #N/A #N/A FALSE FALSE FALSE (Transcriptional coactivator Sp1 10) Fibronectin (FN) (Cold-insoluble globulin) P02751 FN1 (CIG) [Cleaved into: Anasteiiin; Ugl-Y1 ; Ugl- 2386 #N/A #N/A #N/A FALSE FALSE FALSE Y2; Ugl-Y3] Fatty-acid amide hydrolase 2 (EC 3.5.1.99) (Amidase domain-containing protein) Q6G R7 FAAH2 532 #N/A #N/A #N/A FALSE FALSE FALSE (Anandamide amidohydrolase 2) (Oleamide hydrolase 2) Poly(ADP-ribose) glycohydroiase ARH3 (EC Q9NX46 ADPRHL2 3.2.1 .143) (ADP-ribosylhydrolase 3) ([Protein 363 #N/A #N/A #N/A FALSE FALSE FALSE ADP-ribosylarginine] hydrolase-like protein 2) o Intraflagellar transport protein 27 homolog Q9BW83 IFT27 (Putative GTP-binding protein RAY-like) (Rab- 186 #N/A #N/A #N/A FALSE FALSE FALSE ike protein 4) Nuclear factor NF~kappa-B p100 subunit (DNA- binding factor KBF2) (H2TF1) (Lymphocyte translocation chromosome 10 protein) Q00653 NFKB2 (Nuclear factor of kappa light polypeptide 900 #N/A #N/A #N/A FALSE TRUE TRUE gene enhancer in B-celis 2) (Oncogene Lyt- 10) (Lyt10) [Cleaved into: Nuclear factor NF- kappa-B p52 subunit] Histone-lysine N-methyltransferase NSD2 (EC 2.1 . 1 .43) (Multiple myeloma SET domain- containing protein) (MMSET) (Nuclear SET 096028 NSD2 1365 #N/A #N/A #N/A TRUE TRUE FALSE domain-containing protein 2) (Protein irithorax- 5) (Wolf-Hirschhorn syndrome candidate 1 protein) Inhibitor of nuclear factor kappa-B kinase subunit alpha (i~kappa~B kinase alpha) (IKK- A) (IKK-alpha) (IkBKA) (IkappaB kinase) (EC 2.7.1 1 10) (Conserved helix-loop-helix 0151 11 CHUK 745 #N/A #N/A #N/A FALSE TRUE FALSE ubiquitous kinase) (l-kappa-B kinase 1) (IKK1) (Nuclear factor NF-kappa-B inhibitor kinase alpha) (NFKBIKA) (Transcription factor 16) (TCF-16) SH3 and multiple ankyrin repeat domains protein 1 (Shankl) (Somatostatin receptor- Q9Y566 SHANK1 2161 #N/A #N/A #N/A FALSE FALSE FALSE interacting protein) (SSTR-interacting protein) (SSTRIP) E3 ubiquitin-protein ligase HECTD1 (EC 2.3.2.26) (E3 ligase for inhibin receptor) ECTD1 (EULIR) (HECT domain-containing protein 1) 2610 #N/A #N/A #N/A FALSE FALSE FALSE (HECT-type E3 ubiquitin transferase HECTD1) Tapasin (TPN) (TPSN) (NGS-17) (TAP- o 015533 TAP BP 448 #N/A #N/A #N/A TRUE TRUE FALSE -4 associated protein) (TAP-binding protein)

Short/branched chain specific acyl-CoA dehydrogenase, miiochondrial (SBCAD) (EC 1.3.8.5) (2-methyl branched chain acyl-CoA P45954 ACADSB 432 #N/A #N/A #N/A FALSE FALSE FALSE dehydrogenase) (2-IV1EBCAD) (2-methyibutyryl coenzyme A dehydrogenase) (2-methylbutyryl- CoA dehydrogenase)

Q8N201 Integrator complex subunit 1 (Int1) 2190 #N/A #N/A #N/A FALSE FALSE FALSE

Serine/threonine-protein kinase A RK2 (EC 2.7.1 1.1) (EC 2.7.1 1 26) (ELKL motif kinase 1) Q7KZI7 /IARK2 (EMK-1) (MAP/microtubule affinity-regulating 788 #N/A #N/A #N/A FALSE FALSE FALSE kinase 2) (PARI homolog) (PARI homolog b) (Par- 1b) (Parlb)

cAMP-regulated phosphoprotein 2 1 (ARPP- Q9UBL0 ARPP21 21) (Thymocyte cAMP-regulated 812 #N/A #N/A #N/A FALSE FALSE FALSE phosphoprotein) Cathepsin B (EC 3.4.22.1) (APP secretase) (APPS) (Cathepsin B1) [Cleaved Into: P07858 CTSB 339 #N/A #N/A #N/A FALSE FALSE FALSE Cathepsin B light chain; Cathepsin B heavy chain] Histone acetyltransferase p300 (p300 HAT) Q09472 EP300 2414 #N/A #N/A #N/A FALSE FALSE FALSE (EC 2.3.1 .48) (E1A-associated protein p300) Zinc finger and BTB domain-containing protein Q9ULJ3 ZBTB21 1066 #N/A #N/A #N/A FALSE FALSE FALSE 2 1 (Zinc finger protein 295) GA-binding protein alpha chain (GABP subunit Q06546 alpha) (Nuclear respiratory factor 2 subunit 454 #N/A #N/A #N/A FALSE FALSE FALSE alpha) (Transcription factor E4TF1-60)

AP-2 complex subunit alpha-2 ( 0 Da coated vesicle protein C) (Adaptor protein complex AP-2 subunit aipha-2) (Adaptor- related protein complex 2 subunit aipha-2) o (Alpha-adaptin C) (Alpha2-adaptin) (Ciathrin 094973 AP2A2 939 #N/A #N/A #N/A FALSE FALSE FALSE assembly protein complex 2 alpha~C large chain) (Huntingtin yeast partner J) (Hunfingfin- interacting protein 9) (HIP-9) (Huntingtin- interacting protein J) (Plasma membrane adaptor HA2/AP2 adaptin alpha C subunit)

060563 CCNT1 Cydin-T1 (CycT1) (Cyclin-T) 726 #N/A #N/A #N/A FALSE FALSE TRUE Probable asparagine-tRNA ligase, G96I59 NARS2 mitochondrial (EC 6.1.1 .22) (Asparaginyi- 477 #N/A #N/A #N/A FALSE FALSE FALSE tRNA synthetase) (AsnRS) Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.4.19.12) (Deubiquitinating enzyme 11) P51784 USP1 1 963 #N/A #N/A /A FALSE TRUE FALSE (Ubiquitin thioesterase 11) (Ubiquitin-specific- processing protease 11) Q96F63 CCDC97 Coiied-coil domain-containing protein 97 343 #N/A #N/A FALSE FALSE FALSE Cell division cycle protein 27 homolog (Anaphase-promoting complex subunit 3) P30260 CDC27 824 #N/A #N/A #N/A TRUE FALSE TRUE (APC3) (CDC27 homolog) (CDC27Hs) (H- NUC) Probable RNA-binding protein 19 (RNA- Q9Y4C8 RBM1 9 960 #N/A #N/A #N/A FALSE FALSE FALSE binding motif protein 19) Ankyrin repeat and KH domain-containing protein 1 (HiV-1 Vpr-binding ankyrin repeat Q8IWZ3 ANKHD1 2542 #N/A #N/A #N/A FALSE FALSE FALSE protein) (Multiple ankyrin repeats single KH domain) (hMASK) Cytochrome c oxidase assembly protein Q7KZN9 4 10 #N/A #N/A #N/A FALSE FALSE FALSE COX1 5 homolog

Bifunctional UDP-N-acetylglucosamine 2- epimerase/N-acetylmannosamine kinase (UDP-GlcNAc-2-epimerase/ManAc kinase) [Includes: UDP-N-acetylglucosamine 2- Q9Y223 GNE epimerase (hydroiyzing) (EC 3.2. 1.183) (UDP 722 #N/A #N/A #N/A FALSE FALSE FALSE o GicNAc-2-epimerase) (Uridine diphosphate-N acetyiglucosamine-2-epimerase); N- acetylmannosamine kinase (EC 2 .7 .1.60) ( anAc kinase)]

Dolschyl-phosphate beta-giucosyltransferase (DolP-glucosyltransferase) (EC 2.4. 1.117) Q9Y673 ALG5 324 #N/A #N/A #N/A FALSE FALSE FALSE (Asparagine-linked glycosylation protein 5 homolog)

RNA polymerase-associated protein RTF1 Q92541 RTF1 7 10 #N/A #N/A #N/A FALSE FALSE FALSE homolog Galectin-9B (Gal-9B) (Galectin-9-like protein Q3B8N2 LGALS9B 356 #N/A #N/A #N/A FALSE FALSE FALSE A) Pyridoxai phosphate homeostasis protein 094903 PROSC (PLP homeostasis protein) (Proline synthase 275 #N/A #N/A #N/A FALSE TRUE TRUE co-transcribed bacterial homolog protein) FAM160B Q5W0V3 Protein FAM160B1 765 #N/A #N/A #N/A FALSE FALSE FALSE 1

Microtubule-associated protein 1S ( AP 1S) (BPY2-interacting protein 1) (Microtubule- associated protein 8} (Variable charge Y Q66K74 A P1S 1059 #N/A #N/A #N/A FALSE FALSE TRUE chromosome 2-interacting protein 1) (VCY2- interaciing protein 1) (VCY2IP-1) [Cleaved into: AP1S heavy chain; MAP1S light chain] DNA-directed RNA polymerase, mitochondrial 00041 1 POLR T 1230 FALSE FALSE FALSE (MiRPOL) (EC 2.7.7.6) Branched-chain-amino-acid aminotransferase, 0 5382 BCAT2 mitochondrial (BCAT(m)) (EC 2.6.1 .42) 392 FALSE FALSE FALSE (Placental protein 18) (PP18)

Integrin beta-2 (Cell surface adhesion glycoproteins LFA-1/CR3/p1 50,95 subunit P05107 ITGB2 769 F LS Ε F L Ξ F LS EE beta) (Complement receptor C3 subunit beta) (CD antigen CD18) Glutathione S-transferase Mu 1 (EC 2.5.1 .18) (GST HB subunit 4) (GST c!ass-mu 1) P09488 GST 1 218 #N/A #N/A FALSE FALSE FALSE (GSTM1-1) (GSTM1a-1a) (GSTM1b-1b) (GTH4) Leucine-rich repeat flightless-interacting protein 1 (LRR FLN-interacting protein 1) (GC- Q32MZ4 LRRFIP1 808 #N/A #N/A #N/A FALSE FALSE FALSE binding factor 2) (TAR RNA-interacting protein) Presequence protease, mitochondrial (hPreP) Q5JRX3 PIT R 1 (EC 3.4.24.-) (Pitrilysin meta!ioproteinase 1) 1037 #N/A #N/A #N/A FALSE FALSE FALSE (Metalioprotease 1) (hMP1)

ER membrane protein complex subunit 3 Q9P012 E C3 261 #N/A #N/A #N/A FALSE FALSE FALSE (Transmembrane protein 111) Beta/gamma crystallin domain-containing Q9Y4K1 CRYBG1 1723 #N/A #N/A #N/A TRUE FALSE FALSE protein 1 (Absent in melanoma 1 protein) Golgi-specific brefeldin A-resistance guanine Q92538 GBF1 nucleotide exchange factor 1 (BFA-resistant 1859 #N/A #N/A #N/A FALSE FALSE FALSE GEF 1) DNA polymerase alpha catalytic subunit (EC P09884 POLA1 2.7.7 7) (DNA polymerase alpha catalytic 1462 #N/A #N/A #N/A FALSE FALSE FALSE subunit p180)

E3 ubiqustin-proiein ligase UBR1 (EC 2.3.2 27) (N-recognin-1) (RING-type E3 ubiquitin G8IWV7 UBR1 1749 #N/A #N/A #N/A FALSE FALSE FALSE transferase UBR1) (Ubiquitin-protein ligase E3- alpha-1) (Ubiquitin-protein ligase E3-alpha-l)

E3 ubiquitin-protein ligase NEDD4 (EC 2.3.2.26) (Cell proliferation-inducing gene 53 protein) (HECT-type E3 ubiquitin transferase P46934 NEDD4 1319 #N/A #N/A #N/A F FALSE F NEDD4) (Neural precursor cell expressed deveiopmenfaily down-regulated protein 4) (NEDD-4) H ST H2 Histone H2B type 1-J (Histone H2B.1) P06899 126 #N/A #N/A #N/A FA . FALSE FALSE BJ (Histone H2B.r) (H2B/r) Cyclin-dependent kinase 3 (EC 2.7.1 1 22) Q00526 CDK3 3 5 #N/A #N/A #N/A FALSE. FALSE FALSE (Ceil division protein kinase 3) P277Q7 DCK Deoxycytidine kinase (dCK) (EC 2.7 1.74) 260 #N/A #N/A #N/A TRUE FALSE FALSE Argininosuccinate synthase (EC 6.3.4.5) P00966 ASS1 412 #N/A #N/A #N/A FALSE. FALSE FALSE (Citrulline-aspartate ligase) Ethylmalonyl-CoA decarboxylase (EC 4.1 . 1 .94) (Enoyl-CoA hydratase domain- Q9NTX5 ECHDC1 307 #N/A #N/A #N/A FALSE FALSE FALSE containing protein 1) (Methylmalonyi-CoA decarboxylase) ( CD) (EC 4.1 . 1 .41) Acyl-coenzyme A thioesierase 8 (Acyl-CoA thioesterase 8) (EC 3 1.2.27) (Cho!oy!- coenzyme A thioesierase) (HIV-Nef- associated acyl-CoA thioesterase) (PTE-2) O14734 ACOT8 319 #N/A #N/A #N/A FALSE FALSE FALSE (Peroxisomal acyl-coenzyme A thioester hydrolase 1) (PTE-1) (Peroxisomal long-chain acyl-CoA thioesterase 1) (Thioesterase II) (hACTE-lll) (hACTEill) (hTE)

ELMSAN EL 2 and SANT domain-containing protein 1 Q6PJG2 1045 #N/A #N/A #N/A FALSE FALSE FALSE 1 (MIDEAS) Endoplasmic reticLflum-Golgi intermediate Q969X5 ERGIC1 compartment protein 1 (ER-Golgi intermediate 290 #N/A #N/A #N/A FALSE TRUE FALSE compartment 32 kDa protein) (ERGIC-32)

Keratin, type I cuticular Ha1 (Hair keratin, type Q15323 KRT31 416 #N/A #N/A #N/A F LS Ε F L Ξ F LS EE Ha1) (Keratin-31) (K31)

Q9HBU6 ETNK1 Ethanolamine kinase 1 (EKI 1) (EC 2.7.1 .82) 452 #N/A #N/A #N/A FALSE TRUE TRUE

PCI domain-containing protein 2 (CSN12-like Q5JVF3 PC D2 399 #N/A #N/A #N/A FALS Ε FA LS EE FALS EE protein) Kinesin-like protein KIF20A (GG10_2) (Mitotic 095235 KIF20A kinesin-like protein 2) (MKip2) (Rab6- 890 #N/A #N/A #N/A FALSE TRUE TRUE interacting kinesin-like protein) (Rabkinesin-6)

Apolipoprotein L2 (Apoiipoprotein L-ll) (ApoL- Q9BQE5 APOL2 337 #N/A #N/A #N/A FALSE FALSE FALSE

PH and SEC7 domain-containing protein 4 (Exchange factor for ADP-ribosyiation factor guanine nucleotide factor 6 B) (Exchange Q8NDX1 PSD4 1056 #N/A #N/A #N/A FALSE FALSE FALSE factor for ARF6 B) (Pleckstrin homology and SEC7 domain-containing protein 4) (Telomeric of interleukin-1 cluster protein) !nter-alpha-irypsin inhibitor heavy chain H2 ( T! heavy chain H2) (ITI-HC2) (Inter-alpha- inhibitor heavy chain 2) (Inter-alpha-trypsin P19823 ITIH2 946 #N/A #N/A #N/A FALSE FALSE FALSE inhibitor complex component ) (Serum- derived hyaluronan-associated protein) (SHAP)

Zinc finger CCCH-type with G patch domain- containing protein (G patch domain-containing Q8N5A5 ZGPAT protein 6) (Zinc finger CCCH domain- 531 #N/A #N/A #N/A FALSE FALSE FALSE containing protein 9) (Zinc finger and G patch domain-containing protein)

Q8IYL3 C1orf174 UPF0688 protein C1orf 174 243 #N/A #N/A #N/A TRUE FALSE FALSE

Q9H0A8 CO MD4 COMM domain-containing protein 4 199 #N/A #N/A #N/A FALSE FALSE FALSE

Q5JPE7 NOM02 Nodal modulator 2 (pM5 protein 2) 1267 #N/A #N/A #N/A FALSE FALSE TRUE Non-structural maintenance of chromosome Q8WV22 NSMCE1 element 1 homolog (Non-SMC element 1 266 #N/A #N/A #N/A FALSE FALSE FALSE horno!og) (EC 6.3 2.-) Q6NT89 TRNP1 TMF-reguiated nuclear protein 1 227 #N/A #N/A #N/A FALSE FALSE FALSE Q 15036 SNX17 Sorting nexin-17 470 #N/A #N/A #N/A FALSE FALSE FALSE Histone deacetylase 3 (HD3) (EC 3.5.1 .98) 0 15379 HDAC3 428 #N/A #N/A #N/A A S FALSE FALSE (RPD3-2) (SMAP45) Serine/threonine-protein kinase 10 (EC 094804 STK10 968 #N/A #N/A #N/A F S FALSE FALSE 2.7.1 1.1) (Lymphocyte-oriented kinase)

Zinc transporter 7 (ZnT~7) (Solute carrier Q8NEW0 376 #N/A #N/A #N/A FALSE TRUE FALSE family 30 member 7) (Znt-like transporter 2)

Integrator complex subunit 14 (von Wiiiebrand Q96SY0 TS 14 518 #N/A #N/A #N/A FALSE FALSE FALSE factor A domain-containing protein 9)

Torsin-1A (Dystonia 1 protein) (Torsin ATPase- 0 4656 TOR1A 332 #N/A #N/A #N/A TRUE FALSE FALSE 1.A) (EC 3.6.4.-) (Torsin family 1 member A) Mannose-1 -phosphate guanyltransferase alpha (GDP-mannose pyrophospborylase A) Q96IJ6 G PPA 420 #N/A #N/A #N/A FALSE FALSE FALSE (GMPP-alpha) (GTP-mannose-1 -phosphate guanylyltransferase alpha) Prenylcysteine oxidase 1 (EC 1 8.3.5) Q9UHG3 PCYOX1 505 #N/A #N/A #N/A FALSE FALSE FALSE (Prenylcysteine lyase) 075695 RP2 Protein XRP2 350 #N/A #N/A #N/A FALSE FALSE FALSE Ubiquitin-associated domain-containing protein 2 (UBA domain-containing protein 2) Q8NB 4 UBAC2 #N/A #N/A #N/A FALSE TRUE FALSE (Phosphoglycerate dehydrogenase-iike protein 1) HAUS augmin-iike complex subunit 2 Q9NVXQ HAUS2 235 #N/A #N/A #N/A FALSE FALSE FALSE (Centrosomal protein of 27 kDa) (Cep27) Caseinoiytic peptidase B protein homo!og (EC Q9H078 CLPB 3.6.1 .3) (Suppressor of potassium transport 707 #N/A #N/A #N/A FALSE FALSE TRUE defect 3) Ubiquitin-conjugating enzyme E2 E2 (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme Q98LR5 UBE2E2 201 #N/A #N/A #N/A FA S . FALSE FALSE E2) (UbcHS) (Ubiquitin carrier protein E2) (Ubiquitin-protein ligase E2) Protein kinase C alpha type (PKC-A) (PKC- P17252 PRKCA 672 #N/A #N/A #N/A F . FALSE FALSE alpha) (EC 2.7.1 1.13) Solute carrier family 35 member F6 (ANT2- Q8N357 SLC35F6 binding protein) (ANT2BP) (Transport and 371 #N/A #N/A #N/A TRUE FALSE FALSE Golgi organization 9 homolog) Q6Z J NBEAL2 Neurobeachin-like protein 2 2754 #N/A #N/A #N/A FALSE FALSE TRUE Catenin alpha-3 (Alpha T-catenin) (Cadherin- G9UI47 CTNNA3 895 #N/A #N/A #N/A FALSE FALSE FALSE associated protein) Q562R1 ACTBL2 Beta-actin-like protein 2 (Kappa-actin) 376 #N/A #N/A #N/A FALSE FALSE FALSE Histone-lysine N-methyltransferase EZH2 (EC Q15910 EZH2 2.1 . 1 .43) (ENX-1) (Enhancer of zeste homolog 746 #N/A #N/A #N/A FALSE FALSE FALSE 2) (Lysine N-methyltransferase 6) Keratin, type II cytoskeletal 7 1 (Cytokeraiin- 71) (CK-71) (Keraiin-71) (K71) (Type ! inner Q3SY84 KRT71 523 #N/A #N/A #N/A FALSE FALSE FALSE root sheath-specific keratin-K6irs1) (Keratin 6 irs) (hK6irs) (hK6irs1) (Type-I! keratin Kb34) Guanylate-binding protein 1 (EC 3 6.5.-) (GTP- binding protein 1) (GBP-1) (HuGBP-1) P32455 GBP1 (Guanine nucleotide-binding protein 1) 592 #N/A #N/A #N/A FALSE FALSE FALSE (!nterferon-induced guanylate-binding protein 1) TRBV12- P01733 T-celi receptor beta chain V region YT35 135 #N/A #N/A #N/A TRUE FALSE TRUE 3 N-acetylgalactosaminyltransferase 7 (EC 2.4.1 .-) (Polypeptide GaiNAc transferase 7) (GalNAc-T7) (pp-GaNTase 7) (Protein-UDP Q86SF2 GALNT7 657 #N/A #N/A #N/A FALSE FALSE TRUE acetylgalactosaminyltransferase 7) (UDP- Ga!NAc:poiypeptide N ~ acety!galactosaminyltransferase 7) •J\ Dual specificity mitogen-activated protein kinase kinase 3 (MAP kinase kinase 3) (MAPKK 3) (EC 2.7.12.2) (MAPK/'ERK kinase P46734 1AP2K3 347 #N/A #N/A #N/A TRUE TRUE FALSE 3) ( EK 3) (Stress-activated protein kinase kinase 2) (SAPK kinase 2) (SAPKK-2) (SAPKK2)

Transducin-like enhancer protein 3 (Enhancer TLE3 772 #N/A #N/A #N/A TRUE FALSE FALSE of split groucho-like protein 3) (ESG3)

Ribosome-releasing factor 2 , mitochondrial (RRF2mt) (Elongation factor G 2 , 779 #N/A #N/A #N/A FALSE FALSE FALSE mitochondrial) (EF-G2mt) (mEF-G 2) (Elongation factor G2) (hEFG2) Q2TAL8 QRICH1 Glutamine-rich protein 1 776 #N/A #N/A #N/A FALSE TRUE FALSE Q7Z739 YTHDF3 YTH domain-containing family protein 3 585 #N/A #N/A #N/A FALSE FALSE FALSE Cation-dependent rnannose-6-phosphate receptor (CD Man-6-P receptor) (CD-MPR) P20645 277 #N/A #N/A #N/A FALSE TRUE FALSE (46 kDa mannose 6-phosphate receptor) ( PR 46) ATPase family AAA domain-containing protein Q8NBU5 ATAD1 361 #N/A #N/A #N/A FALSE FALSE TRUE 1 (EC 3.6.1.3) (Thorase) Bridging integrator 2 (Breast cancer- Q9UBW5 BIN2 565 #N/A #N/A #N/A FALSE FALSE FALSE associated protein 1) Lysine-specific demetbylase 3B (EC .14.1 .-) (JmjC domain-containing histone Q7LBC6 KD 3B demethyiation protein 2B) (Jumonji domain- 1761 #N/A #N/A #N/A FALSE TRUE FALSE containing protein 1B) (Nuclear protein 5qNCA) RNA polymerase subunit A C-terminal Q9Y5BQ CTDP1 domain phosphatase (EC 3.1 .3.16) (TFIIF- 961 #N/A #N/A #N/A FALSE FALSE FALSE associating CTD phosphatase) Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) (Protein-tyrosine Q06124 PTPN1 1 phosphatase 1D) (PTP-1 D) (Protein-tyrosine 597 #N/A #N/A #N/A FA S . FALSE FALSE phosphatase 2C) (PTP-2C) (SH-PTP2) (SHP- 2) (Shp2) (SH-PTP3)

Q9H6Z4 RANBP3 Ran-binding protein 3 (RanBPS) 567 #N/A #N/A #N/A TRUE FALSE FALSE ,„ Guanine nucleotide-bindinq protein G(o) P09471 GNAQ1 , . . ' 354 #N/A #N/A #N/A F . FALSE FALSE subunit alpha P12755 SKI Ski oncogene (Proto-oncogene c-Ski) 728 #N/A #N/A #N/A FALSE FALSE FALSE Q96C57 C12orf43 Uncharacterized protein C12orf43 262 #N/A #N/A #N/A FALSE FALSE FALSE Cytochrome c oxidase subunit 7A2, mitochondrial (Cytochrome c oxidase subunit P14406 COX7A2 Vlla-liver/heart) (Cytochrome c oxidase 83 #N/A #N/A #N/A FALSE TRUE TRUE subunit V a-L) (Cytochrome c oxidase subunit V aL) Translation initiation factor elF-2B subunit P49770 EIF2B2 beta (S20I15) (S20III15) (elF-2B GDP-GTP 351 #N/A #N/A #N/A FALSE FALSE FALSE exchange factor subunit beta) 043865 RGS10 Regulator of G-protein signaling 10 (RGS10) 173 #N/A #N/A #N/A FALSE FALSE FALSE

U3 small nucleolar ribonucleoprotein protein Q96G21 1P4 IMP4 (U3 snoRNP protein MP4) (Brix domain- 291 #N/A #N/A #N/A FALSE FALSE FALSE containing protein 4) Neuroblast differentiation-associated protein Q09666 5890 #N/A #N/A #N/A FALSE FALSE FALSE A HNA (Desmoyokin) AP2-associated protein kinase 1 (EC 2.7 11 1) Q2M2I8 AAK1 961 #N/A #N/A #N/A FALSE FALSE TRUE (Adaptor-associated kinase 1) Golgi apparatus protein 1 (CFR-1) (Cysteine- rich fibroblast growth factor receptor) (E- Q92896 GLG1 1179 #N/A #N/A #N/A FALSE TRUE FALSE selectin iigand 1) (ESL-1) (Golgi sialoglycoprotein MG-160) Nuclear factor of activated T-cells, cytoplasmic 1 (NF-ATc1) (NFATd) (NFAT transcription 095644 NFATC1 943 #N/A #N/A #N/A F FALSE FA complex cytosoiic component) (NF-ATc) (NFATc) Pro-interieukin-16 [Cleaved into: interieukin-16 Q14005 IL16 (IL-16) (Lymphocyte chemoaftracfant factor) 1332 #N/A #N/A #N/A FALSE FALSE FALSE (LCF)]

SERP B Serpin B8 (Cytoplasmic antiprofeinase 2) P50452 374 #N/A #N/A #N/A FALSE FALSE FALSE 8 (CAP-2) (CAP2) (Peptidase inhibitor 8) (PI-8)

HLA class histocompatibility antigen, alpha P13747 HLA-E 358 #N/A #N/A #N/A FALSE FALSE FALSE chain E ( HC class antigen E) Q9NPB0 SAYSD1 SAYSvFN domain-containing protein 1 183 #N/A #N/A #N/A FALSE FALSE FALSE Q8NC56 LE D2 LE domain-containing protein 2 (hLEM2) 503 #N/A #N/A #N/A FALSE TRUE FALSE Poiycystin-2 (PC2) (Autosomal dominant polycystic kidney disease type II protein) (Polycystic kidney disease 2 protein) Q 13563 PKD2 968 #N/A #N/A #N/A FALSE FALSE FALSE (Polycystwin) (R48321) (Transient receptor potential cation channel subfamily P member 2) EF-hand domain-containing protein D2 Q96C19 EFHD2 240 #N/A #N/A #N/A TRUE FALSE FALSE (Swiprosin-1) Adipocyte plasma membrane-associated Q9HDC9 AP A P 416 #N/A #N/A #N/A FALSE TRUE TRUE protein (Protein BSCv)

NAD(P)H-hydrate epimerase (EC 5.1.99.6) (Apolipoprotein A-l-binding protein) (AI-BP) Q8NCW5 NAXE 288 #N/A #N/A #N/A FALSE FALSE FALSE (NAD(P)HX epimerase) (YjeF N-terminal domain-containing protein 1) (YjeF_N1)

Leucine-rich repeat and calponin homology domain-containing protein 4 (Leucine-rich 075427 LRCH4 683 #N/A #N/A #N/A FALSE FALSE FALSE repeat neuronal protein 4) (Leucine-rich neuronal protein)

NLR family CARD domain-containing protein 3 (CARD'S 5-!ike protein) (Caterpiiler protein Q7RTR2 NLRC3 16.2) (CLR16.2) (NACHT, LRR and CARD 1065 #N/A #N/A #N/A FALSE FALSE TRUE domains-containing protein 3) (Nucleotide- binding oligomerization domain protein 3)

RNA polymerase-associated protein CTR9 Q6PD62 CTR9 1173 #N/A #N/A #N/A FALSE FALSE FALSE homoiog (SH2 domain-binding protein 1)

Antigen peptide transporter 2 (APT2) (ATP- binding cassette sub-family B member 3) (Peptide supply factor 2) (Peptide transporter Q03519 TAP2 PSF2) (PSF-2) (Peptide transporter TAP2) 686 #N/A #N/A #N/A FALSE FALSE FALSE (Peptide transporter involved in antigen processing 2) (Really interesting new gene 11 protein) Monocarboxylate transporter 2 (MCT 2) 060669 SLC16A7 478 #N/A #N/A #N/A FALSE FALSE FALSE (Solute car er family 16 member 7) Vesicle transport protein USE1 (Putative Q9NZ43 USE1 MAPK-activating protein PM26) (USE1-like 259 #N/A #N/A #N/A FALSE FALSE FALSE protein) (p31) Protein Jumonji (Jumonji/ARID domain- Q92833 JA R 2 1246 #N/A #N/A #N/A FALSE FALSE FALSE containing protein 2) Tuftelin-interacting protein 11 (Septin and Q9UBB9 TFIP1 1 837 #N/A #N/A #N/A FALSE FALSE FALSE tuftelin-interacting protein 1) (STIP-1) Queuine tRNA-ribosyliransferase accessory Q9H974 QTRT2 subunit 2 (Queuine tRNA-ribosyliransferase 415 #N/A #N/A #N/A FALSE FALSE FALSE domain-containing protein 1)

ATP-binding cassette sub-family B member 7 , 075027 ABCB7 mitochondrial (ATP-binding cassette 752 #N/A #N/A #N/A FALSE FALSE FALSE transporter 7) (ABC transporter 7 protein)

Serine/threonine-protein kinase TAOS (EC 2 7. 1.1) (Cutaneous T-cell lymphoma- associated antigen HD-CL-09) (CTCL- associated antigen HD-CL-09) (Dendritic cell- Q9H2K8 TAOK3 898 #N/A #N/A #N/A FALSE FALSE FALSE derived protein kinase) (JNK/SAPK-inhibitory kinase) (Jun kinase-inhibitory kinase) (Kinase from chicken homolog A) (hKFC-A) (Thousand and one amino acid protein 3)

Lysine-specific demethyiase 2A (EC 1.14.1 1.27) (CXXC-type zinc finger protein 8) (F-box and leucine-rich repeat protein 11) (F- Q9Y2K7 KD 2A box protein FBL7) (F-box protein Lilina) (F- 1162 #N/A #N/A #N/A FALSE TRUE FALSE box/LRR-repeat protein 11) (JmjC domain- containing histone demethylation protein 1A) ([Histone-H3]-lysine-36 demethyiase 1A)

Serine/threonine-protein kinase WNK1 (EC 2.7.1 1.1) (Erythrocyte 85 kDa protein) (p65) Q9H4A3 WNK1 (Kinase deficient protein) (Protein kinase 2382 #N/A #N/A #N/A FALSE FALSE FALSE lysine-deficient 1) (Protein kinase with no lysine 1) (hVVNKI) CTD small phosphatase-like protein 2 (CTDSP- Q05D32 CTDSP L2 466 #N/A #N/A #N/A FALSE FALSE FALSE like 2) (EC 3.1 .3.-) Leucine-rich repeat-containing protein 36 Q1X8D7 LRRC36 754 #N/A #N/A #N/A FALSE FALSE FALSE (ROR gamma-binding protein 70) Utrophin (Dystrophin-related protein 1) (DRP- P46939 UTRN 3433 #N/A #N/A #N/A FALSE FALSE FALSE 1) K1AA2Q13 Uncharacterized protein KIAA2013 634 #N/A #N/A #N/A FALSE FALSE FALSE Tetratricopeptide repeat protein 37 (TPR repeat protein 37) (SKIS homolog) (Ski3) Q6PGP7 TTC37 1564 #N/A #N/A #N/A FALSE FALSE FALSE (Tricho-hepatic-enteric syndrome protein) (Thespin) 1,4-a!pha-glucan-branching enzyme (EC QQ4446 GBE1 2.4.1 .18) (Brancher enzyme) (Glycogen- 702 #N/A #N/A #N/A FALSE FALSE FALSE branching enzyme) Pyridoxal phosphate phosphatase (PLP Q96GD0 PDXP phosphatase) (EC 3.1 .3.3) (EC 3.1 .3.74) 296 #N/A #N/A #N/A FALSE FALSE FALSE (Chronophin) Q96D05 C10orf35 Uncharacterized protein C10orf35 121 #N/A #N/A #N/A TRUE FALSE FALSE

Q7Z392 Trafficking protein particle complex subunit 11 1133 #N/A #N/A #N/A FALSE FA LSE F 1 Transcription factor / (TCF-7) (T-cell-specific TCF7 384 #N/A #N/A #N/A FALSE FALSE FALSE transcription factor 1) (T-celi factor 1) (TCF-1) o Vacuolar protein sorting-associated protein 18 Q9P253 VPS 18 973 #N/A #N/A #N/A TRUE FALSE FALSE homolog (hVPS18) Cytochrome c oxidase subunit NDUFA4 000483 NDUFA4 (Complex l-MLRQ) (CI-MLRQ) (NADH- 8 1 #N/A #N/A #N/A FALSE FALSE FALSE ubiquinone oxidoreductase MLRQ subunit) Gamma-glutamyl hydrolase (EC 3.4.19.9) Q92820 GGH (Conjugase) (GH) (Gamma-Glu-X 318 #N/A #N/A #N/A TRUE FALSE FALSE carboxypeptidase) Early activation antigen CD69 (Activation inducer molecule) (AIM) (BL-AC/P26) (C-type lectin domain family 2 member C) (EA1) (Early Q07108 CD69 199 #N/A #N/A #N/A TRUE FALSE FALSE T-ce activation antigen p60) (GP32/28) (Leukocyte surface antigen Leu-23) (MLR-3) (CD antigen CD69) Hisione-lysine N-methy!transferase S YD3 (EC 2.1 . 1 .43) (SET and MYND domain- Q9H7B4 SMYD3 428 #N/A #N/A #N/A FALSE FALSE FALSE containing protein 3) (Zinc finger MYND domain-containing protein 1)

Pre-mRNA-processing factor 17 (Cell division 060508 cycle 40 ho o og) (EH-binding protein 3) 579 #N/A #N/A #N/A TRUE FALSE FALSE (Ehb3) (PRP17 homoiog) (hPRP17)

DNA topoisomerase I, mitochondrial Q969P6 TOP1MT 601 #N/A #N/A #N/A FALSE FALSE TRUE (TOPImt) (EC 5.99.1 .2) Peptidy!-prolyl cis-trans isomerase N!MA- interacting 4 (EC 5.2.1 .8) (Parvuiin-14) (Par14) (hPa 4) (Parvulin-17) (Par17) Q9Y237 PIN4 131 #N/A #N/A #N/A FALSE FALSE FALSE (hPar17) (Peptidyl-proiyi cis-trans isomerase Pin4) (PPiase Pin4) (Peptidy!-prolyl cis/trans isomerase EPVH) (hEPVH) (Rotamase Pin4)

N(G),N(G)-dimethylarginine dimethylaminohydrolase 2 (DDAH-2) 095865 DDA H (Dimeihyiarginine dimethylaminohydrolase 2) 285 #N/A #N/A #N/A FALSE. FALSE (EC 3.5.3.18) (DDAHII) (Dimethylargininase-2) (Protein G6a) (S-phase protein)

DBiRD complex subunit ZNF326 (Zinc finger Q5BKZ1 ZNF326 protein 326) (Zinc finger protein interacting 582 #N/A #N/A #N/A FALSE FALSE FALSE with mRNPs and DBC1) Pefiin (PEF protein with a long N-terminal Q9UBV8 PEF1 hydrophobic domain) (Penta-EF hand domain- 284 #N/A #N/A #N/A FALSE FALSE FALSE containing protein 1) AT- ch interactive domain-containing protein 4B (ARID domain-containing protein 4B) (180 kDa Sin3-associated polypeptide) (Sin3- Q4LE39 ARID4B associated polypeptide p180) (Breast cancer- 1312 #N/A #N/A #N/A FALSE FALSE FALSE associated antigen BRCAA1) (Histone deacetylase complex subunit SAP180) (Retinoblastoma-binding protein 1-like 1)

RUN and FYVE domain-containing protein 1 (FYVE-finger protein EIP1) (La-binding protein Q96T51 RUFY1 7 8 #N/A #N/A #N/A FALSE FALSE FALSE 1) (Rab4-interacting protein) (Zinc finger FYVE domain-containing protein 12)

Rab GTPase-activating protein 1 (GAP and RABGAP Q9Y3P9 centrosome-associated protein) (Rab6 1069 #N/A #N/A #N/A FALSE F F 1 GTPase-activating protein GAPCenA)

G-protein-signaling modulator 3 (Activator of Q9Y4H4 GPSIV13 160 #N/A #N/A #N/A FALSE FALSE FALSE G-protein signaling 4) (G 18 1b) (Protein G18)

Myosin-14 (Myosin heavy chain 14) (Myosin Q7Z406 Y H14 heavy chain, non-muscle l e) (Non-muscle 1995 #N/A #N/A #N/A FALSE FALSE FALSE myosin heavy chain lie) (NMHC ll-C)

Protein ELYS (Embryonic large molecule derived from yolk sac) (Protein MEL-28) Q8WYP5 AHCTF1 2266 #N/A #N/A #N/A FALSE TRUE FALSE (Putative AT-hook-containing transcription factor 1)

Segment polarity protein dishevelled homo!og 014641 DVL2 736 #N/A #N/A #N/A FALSE FALSE FALSE DVL-2 (Dishevelled-2) (DSH homo!og 2)

Ras association domain-containing protein 5 (New ras effector 1) (Regulator for cell Q8WWWQ RASSF5 418 #N/A #N/A #N/A FALSE FALSE FALSE adhesion and polarization enriched in lymphoid tissues) (RAPL) ETS-related transcription factor Elf-1 (E74-iike P32519 ELF1 619 #N/A #N/A #N/A FALSE FALSE FALSE factor 1) Q16774 GUK1 Guanyiate kinase (EC 2 7.4.8) (G P kin 197 #N/A #N/A #N/A FALSE FALSE FALSE [F-actin]~meihionine sulfoxide oxidase ICA L1 (EC 1.14.13.225) (Molecule interacting with Q8TDZ2 CAL1 CasL protein 1) (MICAL-1) (NEDD9-interacting 1067 #N/A #N/A #N/A FALSE FALSE FALSE protein with calponin homology and L M domains) Integrin alpha-L (CD1 1 antigen-like family member A) (Leukocyte adhesion glycoprotein P207Q1 !TGAL LFA-1 alpha chain) (LFA-1A) (Leukocyte 1170 #N/A #N/A #N/A FALSE FALSE FALSE function-associated molecule 1 alpha chain) (CD antigen CD1 1a) Guanine nucleotide-binding protein subunit Q14344 GNA13 alpha-13 (G alpha-13) (G-protein subunit 377 #N/A #N/A #N/A FALSE FALSE FALSE alpha-13) Q96AA3 RFT1 Protein RFT1 homolog 541 #N/A #N/A #N/A FALSE FALSE FALSE P60983 G FB G ia maturation factor beta (GMF-beta) 142 #N/A #N/A #N/A FALSE FALSE FALSE CGP9 signalosome complex subunit 6 (SGN6) (Signalosome subunit 6) (JAB1 -containing Q7L5N1 COPS6 327 #N/A #N/A #N/A FALSE FALSE FALSE signalosome subunit 6) ( OV34 homolog) (Vpr-interacting protein) (hVIP)

Q96L92 SNX27 Sorting nexin-27 541 #N/A #N/A #N/A FALSE FALSE FALSE Pre-B-ceH leukemia transcription factor- Q96AQ6 PBXIP1 interacting protein 1 (Hematopoietic PBX- 731 #N/A #N/A #N/A FALSE FALSE FALSE interacting protein) Zinc finger protein 638 (Cutaneous T-ce !ymphoma-assQciated antigen se33-1) (CTCL- Q14966 ZNF638 1978 #N/A #N/A #N/A FALSE FALSE FALSE associated antigen se33-1) (Nuclear protein 220) (Zinc finger matrin-like protein) Guanine nucleotide exchange factor VAV3 Q9UKW4 VAV3 847 #N/A #N/A #N/A FALSE FALSE FALSE (VAV-3) Dynein heavy chain 7 , axonemal (Axonemal beta dynein heavy chain 7) (Ciliary dynein Q8WXX0 DNAH7 4024 #N/A #N/A #N/A FALSE FALSE FALSE heavy chain 7) (Dynein heavy chain-like protein 2) (hDHC2) Peroxisomal membrane protein 1 B (Peroxin- O9601 PEX1 B 1B) (Peroxisomal biogenesis factor 1 B) 259 #N/A #N/A #N/A FALSE FALSE FALSE (Protein PEX1 1 homolog beta) (PEX1 1-beta)

Xaa-Pro dipeptidase (X-Pro dipeptidase) (EC P12955 PEPD 3.4.13.9) (Imidodipeptidase) (Peptidase D) 493 #N/A #N/A #N/A FALSE FALSE FALSE (Proline dipeptidase) (Prolidase)

GRB2-reiated adapter protein 2 (Adapter protein GRID) (GRB-2-iike protein) (GRB2L) (GRBLG) (GRBX) (Grf40 adapter protein) (Grf- 075791 GRAP2 40) (Growth factor receptor-binding protein) 330 #N/A #N/A #N/A FALSE FALSE FALSE (Hematopoietic cell-associated adapter protein GrpL) (P38) (Protein GADS) (SH3-SH2-SH3 adapter Mona) Endonuclease domain-containing 1 protein 094919 ENDOD1 500 #N/A #N/A #N/A FALSE FALSE FALSE (EC 3.1 .30.-) Protein GPR107 (Lung seven transmembrane G5VW38 GPR107 600 #N/A #N/A #N/A FALSE FALSE FALSE receptor 1) Q3 HD2 LS 12 Protein LSM12 homolog 195 #N/A #N/A #N/A FALSE FALSE FALSE Leukocyte surface antigen CD47 (Antigenic surface determinant protein OAS) (integrin- Q08722 CD47 323 #N/A #N/A #N/A FALSE FALSE FALSE associated protein) (IAP) (Protein MER6) (CD antigen CD47) BRISC and BRCA1-A complex member 2 (BRCA1-A complex subunit BRE) Q9NXR7 B.ABAM2 (BRCA1/BRCA2- ∞ ntaining complex subunit 383 #N/A #N/A #N/A FALSE FALSE FALSE 45) (Brain and reproductive organ-expressed protein) Nucleobindin-2 (DNA~binding protein NEFA) P80303 NUCB2 (Gastric cancer antigen Zg4) (Prepronesfatin) 420 #N/A #N/A #N/A FALSE FALSE FALSE [Cleaved into: Nesfatin-11

NEDD4-like E3 ubiquitin-protein ligase WWP2 (EC 2.3 2.26) (Atrophin-1 -interacting protein 2) 000308 WWP2 870 #N/A #N/A #N/A FALSE FALSE FALSE (AIP2) (HECT-type E3 ubiquitin transferase WWP2) (WW domain-containing protein 2)

Q9H0E2 TOLLIP Toll-interacting protein 274 #N/A #N/A #N/A FALSE FALSE FALSE YLP motif-containing protein 1 (Nuclear P49750 YLP 1 1951 #N/A #N/A #N/A FALSE FALSE FALSE protein ZAPS) (ZAP1 13) Cyclin-dependent-like kinase 5 (EC 2.7.1 1.1) (Cell division protein kinase 5) CDK5 (Serine/threonine-protein kinase PSSALRE) 292 #N/A #N/A #N/A FALSE FALSE FALSE (Tau protein kinase catalytic subunit) (TPKII catalytic subunit)

SRSF protein kinase 2 (EC 2.7.1 1.1) (SFRS protein kinase 2) (Serine/arginine-rich protein- •J\ P78362 SRPK2 specific kinase 2) (SR-protein-specific kinase 688 #N/A #N/A #N/A FALSE FALSE FALSE 2) [Cleaved into: SRSF protein kinase 2 N- terminal; SRSF protein kinase 2 C-terminal]

Polymerase delta-interacting protein 2 (38 kDa Q9Y2S7 POLDIP2 DNA polymerase delta interaction protein) 368 #N/A #N/A #N/A FALSE FALSE FALSE (P38) OC A domain-containing protein 2 (Ovarian Q56VL3 OCIAD2 carcinoma immunoreactive antigen-like 154 #N/A #N/A #N/A FALSE FALSE FALSE protein)

Sphingosine-1-pbosphate lyase 1 (S1 PL) (SP- 095470 SGPL1 lyase 1) (SPL 1) (hSPL) (EC 4.1 .2.27) 568 #N/A #N/A #N/A FALSE FALSE FALSE (Sphingosine-1 -phosphate aldolase) Caspase-3 (CASP-3) (EC 3.4 22.56) (Apopain) (Cysteine protease CPP32) (CPP- P42574 CASP3 32) (Protein Yama) (SREBP cleavage activity 277 #N/A #N/A #N/A FALSE FALSE FALSE 1) (SCA-1) [Cleaved into: Caspase-3 subunit p17; Caspase-3 subunit p12] Q13588 GRAP GRB2-re!ated adapter protein 217 #N/A #N/A #N/A FALSE FALSE FALSE Mitochondrial import receptor subunit TOM20 homolog (Mitochondrial 20 kDa outer Q15388 T O 145 #N/A #N/A #N/A FALSE FALSE FALSE membrane protein) (Outer mitochondrial membrane receptor Tom20)

ARHGAP Rho GTPase-activating protein 9 (Rho-type Q9BRR9 750 #N/A #N/A #N/A FALSE FALSE FALSE 9 GTPase-activating protein 9) Choline/ethanoiaminephosphotransferase 1 Q9Y6K0 CEPT1 416 #N/A #N/A #N/A FALSE FALSE FALSE (hCEPTI) (EC 2.7.8.1) (EC 2.7.8.2) TraB domain-containing protein (Protein Q9H4I3 TRABD 376 #N/A #N/A #N/A FALSE FALSE FALSE TTG2 Granzyme A (EC 3.4.21 .78) (CTL tryptase) (Cytotoxic T-lymphocyte proteinase 1) P12544 GZMA 262 #N/A #N/A #N/A FALSE FALSE FALSE (Fragmentin-1) (Granzyme-1) (Hanukkah factor) (H factor) (HF) RNA-binding protein 26 (CTCL tumor antigen Q5T8P6 RBM26 1007 #N/A #N/A #N/A FALSE FALSE FALSE se70-2) (RNA-binding motif protein 26) Leukosialin (Gaiactogiycoprotein) (GALGP) P16150 SPN (Leukocyte sialoglycoprotein) (Sialophorin) 400 #N/A #N/A #N/A FALSE FALSE FALSE (CD antigen CD43) TBC1 domain family member 10A (EBP50- Q9BXI6 PDX interactor of 64 kDa) (EPI64 protein) 508 #N/A #N/A #N/A FALSE FALSE FALSE (Rab27A-GAP-alpha) Arachidonate 5-lipoxygenase-activating P20292 ALOX5AP 161 #N/A #N/A #N/A FALSE FALSE FALSE protein (FLAP) (MK-886-binding protein) U 1 small nuclear ribonucieoprotein A (U1 P09012 SNRPA 282 #N/A #N/A #N/A FALSE FALSE FALSE snRNP A) (U1-A) (U1A) Remodeling and spacing factor 1 (Rsf~1) (HBV pX~associated protein 8) (Hepatitis B virus X- Q96T23 RSF1 1441 #N/A #N/A #N/A FALSE FALSE FALSE associated protein) (p325 subunit of RSF chromatin-remodeling complex)

SH3 domain-binding glutamic acid-rich-like SH3BGR Q9H299 protein 3 (SH3 domain-binding protein 1) 93 #N/A #N/A #N/A FALSE FALSE FALSE L3 (SH3BP-1) Rho guanine nucleotide exchange factor 7 ARHGEF Q14155 (Beta-Pix) (COOL-1) (PAK-interacting 803 #N/A #N/A #N/A FALSE FALSE FALSE 7 exchange factor beta) (p85) 28S ribosomai protein S28, mitochondrial (MRP-S28) (S28mt) (28S ribosomai protein Q9Y2Q9 MRPS28 S35, mitochondrial) (MRP-S35) (S35mt) 187 #N/A #N/A #N/A FALSE FALSE FALSE (Mitochondrial small ribosomai subunit protein bS1m) Q8N9N7 LRRC57 Leucine-rich repeat-containing protein 57 239 #N/A #N/A #N/A FALSE FALSE FALSE Voltage-gated hydrogen channel 1 (Hydrogen Q96D96 HVCN1 voltage-gated channel 1) (HV1) (Voltage 273 #N/A #N/A #N/A FALSE FALSE FALSE sensor domain-only protein) 095149 SNUPN Snurportin-1 (RNA U transporter 1) 360 #N/A #N/A #N/A FALSE FALSE FALSE

Marginal zone B ~ and B -cell-specific protein (Mesenteric estrogen-dependent adipose 7) (MEDA-7) (Plasma cell-induced resident Q8WU39 Ζ Β1 189 #N/A #N/A #N/A FALSE FALSE FALSE endoplasmic reticulum protein) (Plasma cell- induced resident ER protein) (pERpl) (Proapoptotic caspase adapter protein)

ATP synthase subunit e , mitochondrial (ATPase subunit e) [Cleaved into: ATP Ρ56385 ΑΤΡ 5Ι 69 #N/A #N/A #N/A FALSE FALSE FALSE synthase subunit e , mitochondrial, N- terminaliy processed] T-cell-specific surface glycoprotein CD28 Ρ 10747 CD28 220 #N/A #N/A #N/A FALSE FALSE FALSE (TP44) (CD antigen CD28) Hemoglobin subunit delta (Delta-globin) HBD 147 #N/A #N/A #N/A FALSE FALSE FALSE (Hemoglobin delta chain) Thymocyte nuclear protein 1 (Thymocyte Q9P016 ΤΗΥΝ 1 225 #N/A #N/A #N/A FALSE FALSE FALSE protein Thy28) Q8N7X0 Androglobin (Calpain-7-iike protein) 1667 #N/A #N/A #N/A FALSE FALSE FALSE Q658Y4 FAM91A1 Protein FAM91A1 838 #N/A #N/A #N/A FALSE FALSE FALSE Ubiquitin carboxyi-terminal hydrolase 4 (EC 3.4. 9 12) (Deubiquitinating enzyme 4) Q13107 USP4 (Ubiquitin thioesterase 4) (Ubiquitin-specific- 963 #N/A #N/A #N/A FALSE FALSE FALSE processing protease 4) (Ubiquitous nuclear protein homolog) Zinc finger protein Helios (ikaros family zinc Q9UKS7 Z F2 526 #N/A #N/A #N/A FALSE FALSE FALSE finger protein 2) 60S ribosomai protein L26-!ike 1 (Large Q9UNX3 RPL26L1 145 #N/A #N/A #N/A FALSE FALSE FALSE ribosomai subunit protein uL24-like 1) RALGAP Ral GTPase-activating protein subunit beta Q86X10 1494 #N/A #N/A #N/A FALSE FALSE FALSE (p170) Small ubiquitin-related modifier 1 (SUMO-1) (GAP-modifying protein 1) (GMP1) (S T3 Ρ63165 homolog 3) (Sentrin) (Ubiquitin-homology 1 1 #N/A #N/A #N/A F FALSE F domain protein PIC1) (Ubiquitin-like protein SMTSC) (SmtSC) (Ubiquitin-like protein UBL1)

Leukocyte surface antigen CD53 (Cell surface Ρ 19397 CD53 glycoprotein CD53) (Tetraspanin-25) (Tspan- 219 #N/A #N/A #N/A FALSE FALSE FALSE 25) (CD antigen CD53) Ρ01737 T-celi receptor alpha chain V region PY14 135 #N/A #N/A #N/A FALSE FALSE FALSE Glutathione S~transferase C-terminal domain- Q8NEC7 GSTCD 633 #N/A #N/A #N/A F . FALSE FALSE containing protein CDV3 Q9UKY7 Protein CDV3 homolog 258 #N/A #N/A #N/A TRUE FALSE FALSE H41 Tubulin gamma-1 chain (Garnma~1 -tubulin) TUBG1 Ρ23258 (Gamma-tubulin complex component 1) (GCP- 451 #N/A #N/A #N/A FALSE FALSE FALSE TUBG 1) SUZ12 Poiycomb protein SUZ12 (Chromatin CHET9 precipitated E2F target 9 protein) (ChET 9 Q15022 739 #N/A #N/A #N/A FALSE TRUE FALSE JJAZ1 protein) (Joined to JAZF1 protein) K1AA0160 (Suppressor of zeste 12 protein homolog)

043566 RGS14 Regulator of G-protein signaling 14 (RGS14) 566 #N/A #N/A #N/A FALSE FALSE FALSE

Phosphoinositide 3-kinase regulatory subunit PIK3R4 4 (PI3-kinase regulatory subunit 4) (EC Q99570 1358 #N/A #N/A #N/A FALSE FALSE TRUE VPS 15 2.7.1 1.1) (PI3-kinase p150 subunit) (Phosphoinositide 3-kinase adaptor protein) ARHGAP 15 BM- Rho GTPase-activating protein 15 024 BM- (ArhGAP15) (Rho-type GTPase-activating 475 #N/A #N/A #N/A FALSE FALSE FALSE 030 BM- protein 15)

Signaling threshold-regulating transmembrane adapter 1 (SHP2-interacting transmembrane Q9Y3P8 SIT1 SIT 196 #N/A #N/A #N/A TRUE FALSE FALSE adapter protein) (Suppression-inducing transmembrane adapter 1) (gp30/40)

W D repeat-containing protein 6 1 (Meiotic recombination REC14 protein homolog) (SKIS Q9GZS3 WDR61 305 #N/A #N/A #N/A FALSE FALSE TRUE homolog) (Ski8) [Cleaved into: W D repeat- containing protein 6 1, N-terminally processed]

m7GpppX diphosphatase (EC 3.6.1 .59) (DCS- DCPS 1) (Decapping scavenger enzyme) (Hint- DCS1 related 7meGMP-directed hydrolase) Q96C86 337 #N/A #N/A #N/A FALSE FALSE FALSE HINTS (Histidine triad nucleotide-binding protein 5) HSPC015 (Histidine triad protein member 5) (HINT-5) (Scavenger mRNA-decapping enzyme DcpS) BRAT1 BRCA1 -associated ATM activator 1 (BRCA1- Q6PJG6 BAAT1 associated protein required for ATM activation 821 #N/A #N/A #N/A FALSE FALSE FALSE C7orf27 protein 1)

GSTM3 Glutathione S-transferase Mu 3 (EC 2.5.1 18) P21266 225 #N/A #N/A #N/A FALSE FALSE FALSE GST5 (GST class-mu 3) (GSTM3-3) (hGSTM3-3)

NAB2 NGFI-A-binding protein 2 (EGR-1 -binding 4 2 ADER p t 2 ( n - s s c delayed 525 #N/A #N/A #N/A FALSE FALSE FALSE early response protein) (Protein MADER) CYFIP2 Cytoplasmic FMR1 -interacting protein 2 (p53- Α Α 1278 #N/A #N/A #N/A FALSE FALSE FALSE Ί Ί inducible. . .. . protein, . 121) Ρ ΙΚ 1 Ί QQ2447 SP3 Transcription factor Sp3 (SPR-2) 781 #N/A #N/A #N/A FALSE TRUE FALSE PRAF 060831 PRA1 family protein 2 178 #N/A #N/A #N/A F LS Ε F L Ξ F LS EE JM4 Non-structural maintenance of chromosomes NSMCE3 element 3 homolog (Non-SMC element 3 w HCA4 homolog) (Hepatocellular carcinoma- fi 7 3 4 #N/A #N/A #N/A FALSE FALSE FALSE ¾o AGEG1 associated protein 4) (MAGE-G1 antigen) NDNL2 (Melanoma-associated antigen G1) (Necdin- ike protein 2)

[ X37 7 n n ¾7 e ATP-dependent RNA helicase 1157 #N/A #N/A #N/A FALSE FALSE FALSE DHX37 (EC 4 3 ) (DEAH box protein 37) KIAA1517 ' v !

DYNC1 L Cytoplasmic dynein 1 light intermediate chain 043237 2 DNCLI2 2 (Dynein light intermediate chain 2 , cytosolic) 492 #N/A #N/A #N/A FALSE FALSE FALSE L1C2 (LIC-2) (LIC53/55)

Galectin-9 (Gai-9) (Ecalectin) (Tumor antigen 82 LGALS9 355 #N/A #N/A #N/A FALSE FALSE FALSE HOM-HD-21)

PRKD2 Serine/threonine-protein kinase D2 (EC Q9BZL6 PKD2 878 #N/A #N/A #N/A TRUE FALSE FALSE 2.7.1 1.13) (nPKC-D2) HSPC187 Y E1L1 ATP~dependent zinc metalioproiease Y IV E L 1 FTSH1 (EC 3.4 24 .-) (ATP-dependent YME1 L Q96TA2 metalioproiease FtsH1) (Meg-4) (Presenilin- 773 #N/A #N/A #N/A FALSE FALSE FALSE NQ 86 associated metalioprotease) (PA P) (YME1- /PRO430 ike protein 1)

3-hydroxybutyrate dehydrogenase type 2 (EC BDH2 1. 1 . 1 .-) (EC 1.1.1 .30) DHRS6 (Dehydrogenase/reductase SDR family SDR15C1 Q9BUT1 „ member 6) (Oxidoreductase UCPA) (R-beta- 245 #N/A #N/A #N/A FALSE FALSE FALSE UNQ6308l , , , , , , , . hydroxybutyrate dehydrogenase) (Short chasn /PRO209 dehydrogenase/reduciase family 15C member 33 1) mRNA-decapping enzyme 1A (EC 3.-.-.-) DCP1 A Q9NP16 (Smad4-interacting transcriptional co 582 #N/A #N/A #N/A FALSE FALSE FALSE i ll r activator) (Transcription factor S IF)

URB2 Unhealthy ribosome biogenesis protein 2 1524 #N/A #N/A #N/A FALSE FALSE FALSE KIAA0133 homoiog

VPS4B Vacuolar protein sorting-associated protein 4 B SKD1 (EC 3.6.4.6) (Cell migration-inducing gene 1 075351 444 #N/A #N/A #N/A FALSE FALSE FALSE VPS42 protein) (Suppressor of K(+) transport growth MIG1 defect 1) (Protein SKD1)

IK RED Protein Red (Cytokine IK) (IK factor) (Protein Q13123 557 #N/A #N/A #N/A FALSE FALSE FALSE RER RER)

NIP7 CGI- 37 HSPC031 HSPC180 60S ribosome subunit biogenesis protein NIP7 Q9Y221 180 #N/A #N/A #N/A FALSE FALSE FALSE O K SW - homoiog (KD93) cl.76 O K S - cl.78 CDABPOO Beta-2-rnicroglobulin [Cleaved into: Beta~2~ P61769 92 119 #N/A #N/A #N/A FALSE FALSE FALSE microglobulin form p 5.3] HDCMA2 2P

SPATA5 Spermatogenesis-associated protein 5 Q8NB90 AFG2 (ATPase family protein 2 homolog) 893 #N/A #N/A #N/A FALSE FALSE FALSE SPAF (Spermatogenesis-associated factor protein)

Dephospho-CoA kinase domain-containing Q8WVC6 DCAKD 231 #N/A #N/A #N/A FALSE FALSE FALSE protein

(E3-independent) E2 ubiquitin-conjugating enzyme (EC 2.3.2.24) (E2/E3 hybrid ubiquitin- protein ligase UBE20) (Ubiquitin carrier UBE20 Q9C0C9 protein O) (Ubiquitin-conjugating enzyme E2 1292 FALSE FALSE FALSE #N/A #N/A #N/A KIAA1734 O) (Ubiquitin-conjugating enzyme E2 of 230 kDa) (Ubiquitin-conjugating enzyme E2-230K) (Ubiquitin-protein ligase O)

1-phosphatidylinositol 4,5-bisphosphate PLCH1 phosphodiesterase eta-1 (EC 3.1 .4.1 1) Q4KWH8 KIAA1069 (Phosphoinositide phospholipase C-eta-1) 1693 FALSE FALSE FALSE #N/A #N/A #N/A PLCL3 (Phospholipase C-eta-1) (PLC-eta-1) (Phospholipase C-like protein 3) (PLC-L3) RPS16 28S ribosomal protein S18, mitochondrial Q9Y3D3 RPMS16 (MRP-S16) (S16mt) (Mitochondrial small 137 FALSE FALSE FALSE #N/A #N/A #N/A CGI-132 ribosomal subunit protein bS16m)

28S ribosomal protein S18b, mitochondrial MRPS18 (MRP-S18-b) (Mrps18-b) (S18mt-b) (28S B C6orf14 ribosomal protein S18-2, mitochondrial) (MRP- Q9Y676 258 FALSE FALSE FALSE #N/A #N/A #N/A HSPC183 S18-2) (Mitochondrial small ribosomal subunit PTD017 protein bS18b) (Mitochondrial small ribosomal subunit protein mS40) MRPS22 28S ribosomal protein S22, mitochondrial CSorfS P82650 (MRP-S22) (S22mt) (Mitochondrial small 360 FALSE TRUE FALSE #N/A #N/A RPMS22 ribosomal subunit protein mS22) GK002 28S ribosomal protein S26 mitochondrial MRPS26 (MRP-S26) (S26mt) (28S ribosomal protein C20orf19 Q9BYN8 S13, mitochondrial) (MRP-S13) (S13mt) 205 FALSE FALSE FALSE #N/A #N/A 3 (Mitochondrial small ribosomal subunit protein RP S 3 mS26) 28S ribosomal protein S34, mitochondrial P82930 RPS34 (MRP-S34) (S34mt) (Mitochondrial small 218 FALSE FALSE FALSE #N/A #N/A #N/A ribosomal subunit protein mS34) 28S ribosomal protein S5, mitochondrial (MRP P82675 RPS5 S5) (S5mt) (Mitochondrial small ribosomal 430 FALSE FALSE FALSE #N/A #N/A #N/A subunit protein uS5m) 28S ribosomal protein S7, mitochondrial (MRP S7) (S7mt) (Mitochondrial small ribosomal Q9Y2R9 1RPS7 242 FALSE F L FALSE! #N/A #N/A #N/A subunit protein uS7m) (bMRP-27a) (bMRP27a) 2-amino-3-ketobutyrate coenzyme A ligase, GCAT mitochondrial (A KB ligase) (EC 2.3.1 29) 075600 419 FALSE FALSE FALSE #N/A #N/A #N/A KBL (Aminoacetone synthase) (Glycine acetyltransferase) 39S ribosomal protein L mitochondrial MRPL1 1 Q9Y3B7 (L1 1mt) (MRP-L1 ) (Mitochondrial large 192 FALSE FALSE FALSE #N/A #N/A #N/A CGI-1 13 ribosomal subunit protein L 1m) MRPL16 39S ribosomal protein L16, mitochondrial Q9NX20 PNAS- (L16mt) (MRP-L16) (Mitochondrial large 251 FALSE FALSE FALSE #N/A #N/A #N/A 111 ribosomal subunit protein ul_16m) 39S ribosomal protein L19, mitochondrial RPL19 (L19mt) (MRP-L19) (39S ribosomal protein KIAA0104 L15, mitochondrial) (L15mt) (MRP-L15) 292 FALSE FALSE! #N/A #N/A #N/A RPL15 (Mitochondrial large ribosomal subunit protein bL19m) 39S ribosomal protein L2, mitochondrial MRPL2 Q5T653 (L2mt) (MRP-L2) (Mitochondrial large 305 FALSE FALSE FALSE #N/A #N/A #N/A CG!-22 ribosomai subunit protein L2 )

39S ribosomai protein L28 mitochondrial (L28mt) (MRP-L28) (Melanoma antigen p15) 1RPL28 Q 13084 (Melanoma-associated antigen recognized by 256 FALSE FALSE FALSE #N/A #N/A #N/A »IA A T 1 T-iympbocytes) (Mitochondrial large ribosomai subunit protein bL28m)

MRPL3 39S ribosomai protein L3, mitochondrial MRL3 (L3mt) (MRP-L3) (Mitochondrial large 348 FALSE FALSE FALSE #N/A #N/A #N/A RPML3 ribosomai subunit protein uL3m)

MRPL37 39S ribosomai protein L37, mitochondrial MRPL2 (L37mt) (MRP-L37) (39S ribosomai protein L2, Q9BZE1 423 FALSE FALSE FALSE #N/A #N/A #N/A RPML2 mitochondrial) (L2mt) (MRP-L2) (Mitochondrial HSPC235 large ribosomai subunit protein mL37)

39S ribosomai protein L38, mitochondrial MRPL38 Q96DV4 (L38mt) (MRP-L38) (Mitochondrial large 380 FALSE FALSE FALSE #N/A #N/A # /A HSPC262 ribosomai subunit protein mL38)

MRPL4 39S ribosomai protein L4, mitochondrial Q9BYD3 CDABP00 (L4mt) (MRP-L4) (Mitochondrial large 3 11 FALSE FALSE FALSE #N/A #N/A #N/A 9 1 CG!-28 ribosomai subunit protein uL4m)

39S ribosomai protein L45 mitochondrial Q9BRJ2 MRPL45 (L45mt) (MRP-L45) (Mitochondrial large 306 FALSE FALSE FALSE #N/A #N/A #N/A ribosomai subunit protein mL45)

MRPL48 39S ribosomai protein L48, mitochondrial Q96GC5 CGI-1 18 (L48mt) (MRP-L48) (Mitochondrial large 212 FALSE TRUE FALSE #N/A #N/A #N/A HSPC290 ribosomai subunit protein mL48)

39S ribosomai protein L50, mitochondrial Q8N5N7 MRPL50 (L50mt) (MRP-L50) (Mitochondrial large 158 FALSE FALSE FALSE #N/A #N/A #N/A ribosomai subunit protein mL5Q) 3-oxoacyl-[acyl-carrier-protein] synthase, Q9NWU1 OXSM mitochondria! (EC 2.3 1 4 1) (Beta-ketoacyl- 459 FALSE FALSE FALSE #N/A #N/A #N/A ACP synthase) 40S ribosoma! protein S27-like (Small Q7 U 5 RPS27L 84 FALSE FALSE FALSE #N/A #N/A #N/A ribosoma! subunit protein eS27-like) 5'(3')-deoxyribonuc!eotidase, cytosolic type NT5C (EC 3 .1.3.-) (Cytosolic 5',3'-pyrimidine Q8TCD5 DNT1 201 FALSE FALSE FALSE #N/A #N/A #N/A nucleotidase) (Deoxy-5'-nucleotidase 1) (dNT- U PH2 1) N D3 Q96D46 60S ribosoma! export protein NMD3 (hNMDS) 503 FALSE FALSE FALSE #N/A #N/A #N/A CGI-Q7 60S ribosoma! protein L7-!ike 1 (Large Q6DKI1 RPL7L1 246 TRUE FALSE FALSE #N/A #N/A #N/A ribosomal subunit protein uL30-like 1)

Acy!-coenzyme A synthetase ACSM3, mitochondria! (EC 6.2.1 .2) (Acyl-CoA ACS 3 synthetase medium-chain family member 3) Q53FZ2 586 FALSE FALSE FALSE #N/A #N/A #N/A SAH (Butyrate-CoA ligase 3) (Butyry!-coenzyme A synthetase 3) (Middle-chain acyl-CoA •J\ synthetase 3) (Protein SA homolog)

Acyl-coenzyme A thioesterase 3 (Acyi-CoA ACOT13 thioesterase 13) (EC 3.1 .2.-) (Thioesterase THE 2 Q9NPJ3 superfami!y member 2) [Cleaved into: Acyl- 140 FALSE FALSE FALSE #N/A #N/A #N/A HT012 coenzyme A thioesterase 13, N-terminal!y PNAS-27 processed]

Acyl-coenzyme A thioesterase 9 , ACOT9 Q9Y305 mitochondria! (Acyl-CoA thioesterase 9) (EC 439 FALSE FALSE FALSE #N/A #N/A #N/A CG!-16 3.1 .2.-) (Acyi-CoA thioester hydrolase 9) Adenosine 3'-phospho 5'-phosphosu!fate SLC35B2 transporter 1 (PAPS transporter 1) (Putative PAPST1 Q8TB61 MAPK-activating protein P 15) (Putative NF- 432 TRUE FALSE FALSE #N/A #N/A #N/A PSEC014 kappa-B-activating protein 48) (Solute carrier family 35 member B2) Adenylate kinase isoenzyme 1 (AK 1) (EC 2.7.4.3) (EC 2.7.4.6) (ATP-A P transphosphorylase 1) (ATP:AMP 194 FALSE FALSE FALSE #N/A #N/A #N/A phosphotransferase) (Adenylate monophosphate kinase) (Myokinase) Adenylate kinase isoenzyme 6 (AK6) (EC AK6 2.7.4.3) (Adrenal gland protein AD-004) (Coilin- C NAP interacting nuclear ATPase protein) (hCINAP) 172 FALSE TRUE FALSE #N/A #N/A #N/A AD-004 (Dual activity adenylate kinase/ATPase) CG!-137 (AK/ATPase) ARFGAP ADP-ribosylation factor GTPase-activating 2 ZNF289 protein 2 (ARF GAP 2) (GTPase-activating 521 FALSE FALSE FALSE #N/A #N/A #N/A Nbla1053 protein ZNF289) (Zinc finger protein 289) 5 ADP-ribosylation factor-like protein 8B (ADP- ARL8B ribosylation factor-like protein 10C) (Novel ARL10C 186 FALSE FALSE FALSE #N/A #N/A #N/A small G protein indispensable for equal GIE1 chromosome segregation 1)

AFDN Afadin (ALL1 -fused gene from chromosome AF6 protein) (Protein AF-6) (Afadin adherens 1824 FALSE FALSE FALSE #N/A #N/A #N/A MLLT4 junction formation factor)

Aldehyde dehydrogenase X , mitochondrial ALDH1 B 1 (EC 1.2.1 .3) (Aldehyde dehydrogenase 5) ALDH5 517 TRUE FALSE FALSE #N/A #N/A #N/A (Aldehyde dehydrogenase family 1 member ALDHX B1) ALDH2 Aldehyde dehydrogenase, mitochondrial (EC 517 TRUE FALSE FALSE #N/A #N/A #N/A ALD 1.2. 1.3) (ALDH class 2) (ALDH-E2) (ALDHi) Aldo-keto reductase family 1 member C 1 (EC 1. 1 . 1 .-) (20-alpha-hydroxysteroid dehydrogenase) (20-alpha-HSD) (EC 1. 1 . 1 .149) (Chlordecone reductase homolog AKR1C1 HAKRC) (Dihydrodiol dehydrogenase 1/2) DDH 323 TRUE FALSE FALSE #N/A #N/A #N/A (DD1/DD2) (High-affinity hepatic bile acid- DDH1 binding protein) (HBAB) (Indanol dehydrogenase) (EC 1.1 . 1 . 1 12) (Trans-1,2- dihydrobenzene-1 ,2-dioi dehydrogenase) (EC 1.3.1 .20)

AJdo-keto reductase family 1 member C2 (EC 1.-.-.-) (3~alpha-HSD3) (Chlordecone reductase homolog HAKRD) (Dihydrodiol dehydrogenase 2) (DD-2) (DD2) (Dihydrodiol AKR1C2 P52895 dehydrogenase/bile acid-binding protein) 323 FALSE FALSE FALSE #N/A #N/A #N/A DDH2 (DD/BABP) (Trans-1 ,2-dihydrobenzene-1 ,2-

dio dehydrogenase) (EC 1.3.1 .20) (Type 1 1 3- alpha-hydroxysteroid dehydrogenase) (EC 1. 1 . 1 .357)

ADD1 Alpha-adducin (Erythrocyte adducin subunit P3561 737 FALSE FALSE FALSE #N/A #N/A #N/A ADDA alpha) Alpha-crystallin A chain (Heat shock protein CRYAA beta~4) (HspB4) [Cleaved into: AJpha-crystailin P02489 CRYA1 173 FALSE FALSE FALSE #N/A #N/A #N/A A(1-172); Alpha-crystailin A(1-168); Alpha- HSPB4 crystallin A(1-162)] TFCP2 A pha g obin transcription factor CP2 (SAA3 Q12800 502 FALSE FALSE FALSE #N/A #N/A # /A LSF SEF enhancer factor) (Transcription factor LSF)

Aminoacylase-1 (ACY-1) (EC 3.5 1.14) (N-acyl- Q03154 ACY1 408 FALSE FALSE FALSE #N/A #N/A #N/A L-amino-acid amidohydrolase) Amyloid-like protein 2 (APLP-2) (APPH) APLP2 31 (Amyloid protein homolog) (CDEI box-binding 763 FALSE FALSE FALSE #N/A #N/A #N/A APPL2 protein) (CDEBP) Anaphase-promoiing complex subunit 1 ANAPC1 (APC1) (Cyclosome subunit 1) (Mitotic Q9H1A4 1944 FALSE FALSE FALSE #N/A #N/A #N/A TSG24 checkpoint regulator) (Testis-specific gene 24 protein) Q9Y679 AUP1 Ancient ubiquitous protein 1 476 TRUE TRUE FALSE #N/A #N/A #N/A Ankyrin repeat domain-containing protein 7 ANKRD17 (Gene trap ankyrin repeat protein) 075179 GTAR 2603 TRUE TRUE TRUE #N/A #N/A #N/A (Serologically defined breast cancer antigen KIAA0697 NY-BR-16) ANK1 Ankyrin-1 (ANK-1) (Ankyrin-R) (Erythrocyte P16157 1881 FALSE FALSE FALSE #N/A #N/A #N/A ANK ankyrin) Ankyrin-2 (ANK-2) (Ankyrin-B) (Brain ankyrin) Q01484 ANK2 3957 FALSE FALSE FALSE #N/A #N/A #N/A (Non-erythroid ankyrin)

C12orf3 Q9NQ9Q Anoctamin-2 (Transmembrane protein 16B) 1003 FALSE FALSE FALSE #N/A #N/A #N/A T E 16 B

AP-2 complex subunit sigma (Adaptor protein complex AP-2 subunit sigma) (Adaptor-related protein complex 2 subunit sigma) (Clathrin AP2S1 assembly protein 2 sigma small chain) P53680 AP17 142 TRUE FALSE FALSE #N/A #N/A #N/A (Clathrin coat assembly protein AP17) CLAPS2 (Clathrin coat-associated protein AP17) (HA2 7 kDa subunit) (Plasma membrane adaptor AP-2 17 kDa protein) (Sigma2-adaptin)

AP-3 complex subunit mu-1 (AP-3 adaptor complex mu3A subunit) (Adaptor-related Q9Y2T2 APS? 418 TRUE FALSE FALSE #N/A #N/A #N/A protein complex 3 subunit mu-1) (Mu-adaptin 3A) (Mu3A-adaptin)

ACAP2 Arf-GAP with coiled-coil, ANK repeat and PH CENTB2 domain-containing protein 2 (Centaurin-beta- 778 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0041 2) (Cnt-b2) Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 (AGA.P-3) (CRAI AGAP3 Q96P47 associated GTPase) (CRAG) (Centaurin- 875 FALSE FALSE FALSE #N/A #N/A #N/A CENTG3 gamma-3) (Cnt-g3) (MR -interacting protein) (MRIP-1) ARAP1 Arf-GAP with Rho-GAP domain, ANK repeat Q96P48 CENTD2 and PH domain-containing protein 1 1450 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0782 (Centaurin-deita-2) (Cnt-d2) Arginase-1 (EC 3.5.3.1) (Liver-type arginase) P05089 ARG1 322 FALSE FALSE FALSE #N/.A #N/A #N/A (Type ! arginase) ARMC1 Q9NVT9 Armadillo repeat-containing protein 1 282 FALSE FALSE FALSE #N/A #N/A #N/A ARCP ATX 2 Aiaxin-2 (Spinocerebellar ataxia type 2 ATX2 Q99700 protein) (Trinucleotide repeat-containing gene 1313 TRUE FALSE FALSE #N/A #N/A #N/A SCA2 3 protein) TNRC13 Atlastin-2 (EC 3.6.5.-) (ADP-ribosylation factor ATL2 Q8NHH9 like protein δ-interaciing protein 2) (ARL-6- 583 FALSE TRUE TRUE #N/A #N/A # /A ARL61P2 interacting protein 2) (Aip-2) ATPIF1 A.TPase inhibitor, mitochondrial (inhibitor of Q9UII2 106 FALSE FALSE FALSE #N/A #N/A #N/A ATP F(1)F(o)-ATPase) (IF(1)) (IF1)

ATP-binding cassette sub-family B member 6 , ABCB6 mitochondrial (Mitochondrial ABC transporter MTABC3 Q9NP58 3) (Mt-ABC transporter 3) (P-giycoproiein- 842 FALSE FALSE FALSE #N/A #N/A #N/A reiated protein) (Ubiquitously-expressed U AT mammalian ABC half transporter)

ATP-dependent 8~phosphofructokinase, muscle type (ATP-PFK) (PFK-M) (EC PFKM P08237 2.7.1 . 1 1) (6-phosphofructokinase type A) 780 FALSE FALSE FALSE #N/A #N/A #N/A PFKX {Phosphofructo-1 -kinase isozyme A) (PFK-A) (Phosphohexokinase) DDX19B ATP-dependent RNA he!icase DDX19B (EC DBP5 Q9UMR2 3.6.4.13) (DEAD box RNA he!icase DEADS) 479 FALSE FALSE FALSE #N/A #N/A #N/A DDX19f- r (DEAD box protein 19B) TDBP ATP-dependent RNA he!icase SUPV3L1 , SUPV3L1 YB8 QUV3 to c 3.6.4.13) (Suppressor of 786 FALSE FALSE FALSE #N/A #N/A #N/A varl 3-iike protein 1) (SUV3-iike protein 1)

AR1D3A AT-rich interactive domain-containing protein DRIL1 3A (ARID domain-containing protein 3A) (B- DRIL3 ceil regulator of gH transcription) (Bright) 593 TRUE TRUE FALSE #N/A #N/A #N/A DRX (Dead ringer-like protein 1) (E2F-binding E2FBP1 protein 1) BH3-interacting domain death agonist (p22 BID) (BID) [Cleaved into: BH3-inieracting domain death agonist p15 (p15 BID); BH3- P55957 BID 195 FALSE FALSE FALSE #N/A #N/A #N/A inferacting domain death agonist p13 (p13 BID); BH3-interacting domain death agonist o p 1 l ' (p1 1 BID)] Bifunctional coenzyme A synthase (CoA synthase) (NBP) (POV-2) [Includes: Phosphopantetheine adenylyltransferase (EC COASY 2.7.7.3) (Dephospho-CoA pyrophosphorylase) Q13057 PSEC010 564 FALSE FALSE FALSE #N/A #N/A #N/A (Pantetheine-phosphate adenylyltransferase) (PPAT); Dephospho-CoA kinase (DPCK) (EC 2.7.1 .24) (Dephosphocoenzyme A kinase) (DPCOAK)] Ribosomal oxygenase 2 (60S ribosomal protein L27a hisiidine hydroxylase) RiOX2 (Bifunctiona! Iysine-specific demethylase and D G histidyl-hydroxylase MINA) (EC 1.14.1 1.-) G8IUF8 NA 465 FALSE FALSE FALSE #N/A #N/A #N/A (Histone lysine demethylase MINA) (MYC- M A53 induced nuclear antigen) (Mineral dust- N052 induced gene protein) (Nucleolar protein 52) (Ribosomal oxygenase MINA) (ROX)

BLM Bloom syndrome protein (EC 3.6.4.12) (DNA P54132 RECQ2 heiicase, RecQ-like type 2) (RecQ2) (RecQ 1417 FALSE FALSE FALSE #N/A #N/A #N/A RECQL3 protein- 3) BMP2K BIKE BMP-2-inducibie protein kinase (BIKe) (EC Q9NSY1 1161 FALSE FALSE FALSE #N/A #N/A #N/A HRIHFB2 2.7.1 1.1) 17 BUBS-interacting and GLEBS motif-containing ZNF2Q7 043670 protein ZNF207 (BuGZ) (hBuGZ) (Zinc finger 478 FALSE FALSE FALSE #N/A #N/A #N/A BUGZ protein 207) Calcineurin B homologous protein 1 (Calcineurin B-iike protein) (Calcium-binding CHP1 Q99653 protein CHP) (Calcium-binding protein p22) 195 FALSE TRUE FALSE #N/A #N/A #N/A CHP (EF-hand calcium-binding domain-containing protein p22) Calcium-binding mitochondrial carrier protein SLC25A1 Aralar2 (Citrin) (Mitochondrial aspartate Q9UJSQ 3 675 FALSE FALSE FALSE #N/A #N/A #N/A glutamate carrier 2) (Solute carrier family 25 ARALAR2 member 13) Calpain-2 catalytic subunit (EC 3 4.22.53) (Calcium-activated neutral proteinase 2) CAPN2 P17655 (CANP 2) (Calpain M-type) (Calpain large 700 FALSE FALSE FALSE #N/A #N/A #N/A CANPL2 polypeptide L2) (Calpain-2 large subunit) (Miliimoiar-calpain) (M-calpain) 043852 CALU Calumenin (Crocaibin) ( EF SSP 9302) 315 FALSE FALSE FALSE #N/A #N/A #N/A PRKAR2 cAMP-dependeni protein kinase type H-aipha P13861 A 404 FALSE FALSE TRUE #N/A #N/A #N/A regulatory subunit PK A K PRKAR2 cAMP-dependent protein kinase type H-beta P31323 418 TRUE TRUE TRUE #N/A #N/A #N/A Bb regulatory subunit Cancer/testis antigen family 45 member A 0 P0DMU9 CT45A10 189 FALSE FALSE FALSE #N/A #N/A #N/A (Cancer/testis antigen 45A10) Carbohydrate-responsive element-binding MLXIPL protein (ChREBP) (Class D basic he ix- oop- BHLHD14 helix protein 14) (bHLHd14) (MLX interactor) Q9NP71 M!O (MLX-interacting protein-!ike) (WS basic-helix 852 FALSE FALSE FALSE #N/A #N/A #N/A WBSCR1 loop-helix leucine zipper protein) (WS-bHLH) 4 (Wiliiams-Beuren syndrome chromosomal region 14 protein)

CAS Carbonic anhydrase-related protein (CARP) P35219 290 FALSE FALSE FALSE #N/A #N/A #N/A CALS (Carbonic anhydrase V I) (CA-VIII)

Carbonyl reductase [NADPH] 3 (EC 1. 1 . 1 .184) (NADPH-dependent carbonyl reductase 3) 075828 CBR3 277 FALSE FALSE FALSE #N/A #N/A #N/A (Short chain dehydrogenase/reductase family 2 1C member 2) Carboxymefhylenebutenoiidase homoiog (EC Q96DG6 C BL 245 FALSE FALSE FALSE #N/A #N/A #N/A 3.1 .-.-) Carboxypeptidase D (EC 3.4.17.22) Q75976 CPD 1380 FALSE FALSE FALSE #N/A #N/A #N/A (Metaliocarboxypeptidase D) (gp180) CTNNA2 Catenin aipha-2 (Alpha N-cafenin) (Alpha- P26232 953 FALSE FALSE FALSE #N/A #N/A #N/A CAPR catenin-related protein) Catenin delta-1 (Cadherin-associated Src CTNND1 substrate) (CAS) (p120 catenin) (p120(ctn)) 968 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0384 (p120(cas)) CCAAT/enhancer-binding protein beta (C/EBP CEBPB beta) (Liver activator protein) (LAP) (Liver- TCF5 345 FALSE FALSE FALSE #N/A #N/A #N/A enriched inhibitory protein) (L P) (Nuclear PP9092 factor NF-IL6) (Transcription factor 5) (TCF-5)

CD2-associated protein (Adapter protein Q9Y5K6 CD2AP 639 FALSE FALSE FALSE #N/A #N/A #N/A CMS) (Cas iigand with multiple SH3 domains)

TRIP1Q Cdc42-interacting protein 4 (Protein Feiic) CIP4 (Salt tolerant protein) (hSTP) (Thyroid Q15642 6 1 FALSE FALSE FALSE #N/A #N/A #N/A STOT receptor-interacting protein 1 ) (TR-interacting STP protein 10) (TRIP-10) Cell cycle checkpoint control protein RAD9A RAD9A (hRAD9) (EC 3.1 . 1 1.2) (DNA repair 391 FALSE FALSE FALSE #N/A #N/A #N/A exonuciease rad9 homolog A)

CDC45L . Cell division control protein 45 homolog 566 FALSE FALSE FALSE #N/A #N/A #N/A UNQ374/ (PORC-PI-1) PRO710

CENPH Centromere protein H (CENP-H) (Interphase Q9H3R5 247 TRUE TRUE FALSE #N/A #N/A #N/A ICEN35 centromere complex protein 35)

CLCC1 „ . ~ Chloride channel CLIC-iike protein 1 (Mid-1- Q i 551 FALSE FALSE FALSE #N/A #N/A #N/A related chloride channel protein 1) CLC Chloride intracellular channel protein 2 CLIC2 247 TRUE TRUE FALSE #N/A #N/A #N/A (XAP121) CHPT1 Cholinephosphotransferase 1 (hCPT1) (EC Q8WUD6 CPT1 2.7.8.2) (AAPT1-like protein) (Diacylglyceroi 406 FALSE TRUE FALSE #N/A #N/A #N/A MSTP022 cholinephosphotransferase 1) Chromodomain-helicase-DNA-binding protein 014647 CHD2 2 (CHD-2) (EC 3.6.4.12) (ATP-dependent 1828 FALSE FALSE FALSE #N/A #N/A #N/A helicase CHD2) Chromosome-associated kinesin KIF4B Q2VIQ3 KIF4B 1234 FALSE TRUE FALSE #N/A #N/A # /A (Chromokinesin-B)

Cleavage stimulation factor subunit 1 (CF-1 50 Q05048 CSTF1 kDa subunit) (Cleavage stimulation factor 50 431 FALSE FALSE FALSE #N/A #N/A #N/A kDa subunit) (CSTF 50 kDa subunit) (CstF-50)

CLASRP SFRS16 CLK4-associating serine/arginine rich protein SWAP2 Q8N2 8 (Splicing factor, arginine/serine-rich 16) 674 FALSE FALSE FALSE #N/A #N/A #N/A UNQ2428UNQ242? (Suppressor of white-apricot homolog 2) /PR0498

COPZ Coatomer subunit zeta-1 (Zeta-1 -coat protein) P61923 177 FALSE FALSE FALSE #N/A #N/A #N/A CGI-120 (Zeta-1 COP) HSPC181

Cob(l)yrinic acid a,c-diamide adenosyltransferase, mitochondrial (EC Q96EY8 MMAB , ,. . . . , 250 FALSE FALSE FALSE #N/A #N/A #N/A 2.5.1c 17) (Cob(l)alamin adenosyltransferase) (Methylmalonic aciduria type B protein)

CCDC6 Coiied-coil domain-containing protein 6 Q16204 D10S170 (Papillary thyroid carcinoma-encoded protein) 474 FALSE FALSE FALSE #N/A #N/A #N/A TST1 (Protein H4)

CCDC71 L Q8N9Z2 Coiied-coil domain-containing protein 7 L 235 FALSE FALSE FALSE #N/A #N/A #N/A C7orf74

Coiied-coil domain-containing protein 86 CCDC86 Q9H6F5 (Cytokine-induced protein with coiied-coil 360 FALSE FALSE FALSE #N/A #N/A #N/A domain) COIL P38432 . Coi in (p80-coilin) 576 TRUE FALSE FALSE #N/A #N/A #N/A

LYR 7 Complex HI assembly factor LYRM7 (LYR Q5U5X0 C5orf31 1 4 FALSE FALSE FALSE #N/A #N/A #N/A motif-containing protein 7) Z M 1L Corepressor interacting with RBPJ 1 (CBF1- Q86X95 CIR1 C!R 450 FALSE FALSE FALSE #N/A #N/A # /A interacting corepressor) (Recepin) Cornifin-A (19 kDa pancornulin) (SPRK) P35321 SPRR1A 89 FALSE FALSE FALSE #N/A #N/A #N/A (Small proline-rich protein IA) (SPR-IA) Cornifin-B (14 9 kDa pancornulin) (Small P22528 SPRR1 B 89 FALSE FALSE FALSE #N/A #N/A #N/A proline-rich protein IB) (SPR-IB)

Q9BR76 COR01B Coronin-1 B (Coronin-2) 489 FALSE FALSE FALSE #N/A #N/A #N/A CKB Creatine kinase B-type (EC 2 7.3.2) (B-CK) P12277 381 FALSE FALSE FALSE #N/A #N/A #N/A CKBB (Creatine kinase B chain) Q13616 CUL1 Cullin-1 (CUL-1) 776 FALSE FALSE FALSE #N/A #N/A #N/A CUL5 Cullin-5 (CUL-5) (Vasopressin-activated Q93034 780 FALSE FALSE FALSE #N/A #N/A #N/A VAC 1 calcium-mobilizing receptor 1) (VACM-1) CCNDBP Cyclin-D1-binding protein 1 (Grap2 and cyclin- 1 DIP1 095273 D-interacting protein) (Human homolog of 360 FALSE FALSE FALSE #N/A #N/A #N/A Maid) HH Cyclin-dependent kinase 20 (EC 2.7.1 .22) 4- •J\ (CDK-activating kinase p42) (CAK-kinase p42) (Cell cycle-related kinase) (Cell division Q8IZL9 CCRK 346 F S ! F F L #N/A #N/A #N/A protein kinase 2 ) (Cyclin-dependent protein CDCH kinase H) (Cyclin-kinase-activating kinase p42)

Cysiathionine beta-synthase-like protein (EC P0DN79 CBSL 551 FALSE FALSE FALSE #N/A #N/A # /A 4.2.1 22) (Beta-thionase) (Serine sulfhydrase)

Cystathionine gamma-iyase (EC 4.4.1 1) P32929 CTH (Cysteine- rote n sulfhydrase) (Gamma- 405 FALSE FALSE FALSE #N/A #N/A # /A cystathionase) NFS1 N FS Cysteine desulfurase, mitochondrial (EC Q9Y697 457 FALSE FALSE FALSE #N/A #N/A #N/A HUSSY- 2.8.1 .7) Cytochrome b-245 light chain (Cytochrome b(558) alpha chain) (Cytochrome b558 subunit alpha) (Neutrophil cytochrome b 22 kDa 195 FALSE FALSE FALSE #N/A #N/A #N/A polypeptide) (Superoxide-generating NADPH oxidase light chain subunit) (p22 phagocyte B- cytochrome) (p22-phox) (p22phox)

COA3 Cytochrome c oxidase assembly factor 3 CCDC56 homo!og, mitochondrial (Coiied-coii domain- MITRAC1 containing protein 56) (Mitochondrial 106 TRUE FALSE FALSE #N/A #N/A #N/A 2 translation regulation assembly intermediate HSPC009 of cytochrome c oxidase protein of 2 kDa)

COA7 Cytochrome c oxidase assembly factor 7 (Beta- C1orf163 lactamase hep-like protein) (Respiratory chain 231 FALSE FALSE FALSE #N/A #N/A #N/A RESA1 assembly factor 1) (Sell repeat-containing SELRC1 protein 1) Cytochrome c oxidase subunit 5B, COX5B mitochondrial (Cytochrome c oxidase 129 TRUE FALSE FALSE #N/A #N/A # /A polypeptide Vb) CTU2 Cytoplasmic tRNA 2-thiolation protein 2 C18orf84 515 FALSE FALSE FALSE #N/A #N/A # /A (Cytosolic thiouridylase subunit 2) NCS2 NUBP1 Cytosolic Fe-S cluster assembly factor NUBP1 NBP 320 FALSE FALSE FALSE #N/A #N/A #N/A (Nucleotide-binding protein 1) (NBP 1) NBP1 DAXX Death domain-associated protein 6 (Daxx) BING2 (hDaxx) (ETS1 -associated protein 1) (EAP1 740 FALSE FALSE FALSE #N/A #N/A #N/A DAP6 (Fas death domain-associated protein)

Dedicator of cytokinesis protein 11 (Activated DOCK1 1 Cdc42-associated guanine nucleotide 2 73 FALSE TRUE FALSE #N/A #N/A #N/A ZIZ2 exchange factor) (ACG) (Zizimin-2) DOCKS Dedicator of cytokinesis protein 8 2099 FALSE FALSE FALSE #N/A #N/A #N/A Deoxynucleoside triphosphate triphosphohydro!ase SAMHD1 (dNTPase) (EC SAMHD1 3.1 .5 -) (Dendritic cell-derived IFNG-induced Q9Y3Z3 626 FALSE FALSE FALSE #N/A #N/A #N/A MOPS protein) (DCIP) (Monocyte protein 5) (MOP-5) (SAM domain and HD domain-containing protein 1) Deoxynucleotidy!transferase terminal- interacting protein 2 (Estrogen receptor- DNTTIP2 binding protein) (LPTS-interacting protein 2) Q5QJE6 ERBP 756 FALSE FALSE FALSE #N/A #N/A #N/A (LPTS-RP2) (Terminal TDIF2 deoxynudeotidyltransferase-interacting factor 2) (TdlF2) (TdT-interacting factor 2) Diablo homolog, mitochondrial (Direct IAP- DIABLO binding protein with low pi) (Second Q9NR28 239 TRUE FALSE FALSE #N/A #N/A #N/A SMAC mitochondria-derived activator of caspase) (Smac) Diphosphoinositol polyphosphate UDT P s P h d s (DIPP-1) (EC 3.6.1 .52) (Diadenosine 5',5'"-P1 ,P6-hexaphosphate 095989 D PP 172 FALSE FALSE FALSE #N/A #N/A #N/A hydrolase 1) (EC 3.6.1 .-) (Nucleoside DIPP1 diphosphate-linked moiety X motif 3) (Nudix motif 3) Diphosphoinositol polyphosphate NUDT4 phosphohydrolase 2 (DIPP-2) (EC 3.6.1 .52) DIPP2 (Diadenosine 5',5'"-P1 ,P6-hexaphosphate Q9NZJ9 KIAA0487 180 FALSE FALSE FALSE #N/A #N/A #N/A hydrolase 2) (EC 3.6.1 -) (Nucleoside HDCMB4 diphosphate-linked moiety X motif 4) (Nudix 7P motif 4) APOBEC DNA dC->dU-editing enzyme APOBEC-3C 3C Q9NR 3 C (A3C) (EC 3.5.4,) (APOBE - e) (Phorboin 190 FALSE FALSE FALSE #N/A #N/A #N/A 1L PB DNA mismatch repair protein Msh2 (hMSH2) MSH2 934 FALSE FALSE FALSE #N/A #N/A #N/A (MutS protein homolog 2) DNA mismatch repair protein sh6 (hMSH6) SH6 (G/T mismatch-binding protein) (GTBP) P52701 1360 FALSE FALSE FALSE #N/A #N/A #N/A GTBP (GTMBP) (MutS protein homo!og 6) (MutS- a pha 160 kDa subunit) (p160) PR 2 DNA primase large subunit (EC 2.7.7.-) (DNA P49643 509 TRUE FALSE FALSE #N/A #N/A #N/A PRIM2A primase 58 kDa subunit) (p58) DNA-directed RNA polymerase subunit POLR1 E RPA49 (RNA polymerase subunit A49) (DNA- Q9GZS1 PAF53 directed RNA polymerase I subunit E) (RNA 481 TRUE FALSE FALSE #N/A #N/A #N/A PRAF1 polymerase l-associated factor 1) (RNA polymerase l-associated factor 53)

DNA-directed RNA polymerase IN subunit RPC2 (RNA polymerase I subunit C2) (EC Q9NW08 POLR3B 2.7.7.6) (C128) (DNA-directed RNA 1133 FALSE FALSE FALSE #N/A #N/A #N/A

polymerase 11 127.6 kDa polypeptide) (DNA- directed RNA polymerase I I subunit B) 4- Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha- 1,3-mannosyltransferase (EC 2.4.1 .258) (Asparagine-iinked glycosylation protein 3 ALG3 homoiog) (Doi-P-Man~dependent alpha(1-3)- Q92685 NOT mannosyltransferase) (Doiichyi-P- 438 FALSE FALSE FALSE #N/A #N/A #N/A NOT56L Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase) (Dolichyl-phospbate- mannose-glycolipid alpha- mannosyltransferase) (Not56-!ike protein)

Double-strand break repair protein RE11 MRE1 1 (Double-strand break repair protein MRE1 A) HNGS1 (Meiotic recombination 11 homoiog 1) (MRE1 1 708 TRUE FALSE FALSE #N/A #N/A #N/A RE1 A homoiog 1) (Meiotic recombination 1 homoiog A) (MRE1 1 homoiog A) Dynein heavy chain 17, axonemai (Axonernal beta dynein heavy chain 17) (Axonernal DNAH17 dynein heavy chain-like protein 1) (Ciliary Q9UFH2 DNAHL1 4485 FALSE FALSE FALSE #N/A #N/A #N/A dynein heavy chain 17) (Ciliary dynein heavy DNEL2 chain-like protein 1) (Dynein light chain 2 , axonernal) Dynein light chain 2 , cytoplasmic (8 kDa DYNLL2 Q96FJ2 dynein light chain b) (DLC8b) (Dynein light 89 FALSE FALSE FALSE #N/A #N/A #N/A DLC2 chain LC8-type 2)

ZNF451 COASTE E3 SUMO-protein ligase ZNF451 (EC 6.3.2.-) Q9Y4E5 R (Coactivator for steroid receptors) (Zinc finger 1061 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0576 protein 451) K1AA17Q2

E3 ubiqLfitin-protein ligase CHIP (EC 2.3.2.27) 4- (Antigen NY-CO-7) (CLL-associated antigen STUB1 KW-8) (Carboxy terminus of Hsp70-interacting Q9UNE7 CHIP 303 TRUE TRUE FALSE #N/A #N/A #N/A protein) (RING-type E3 ubiquitin transferase PP1 131 CHIP) (STIP1 homology and U box-containing protein 1)

LTN1 C21orf1Q E3 ubiquitin-protein ligase iisterin (EC C21orf98 2.3.2.27) (RING finger protein 160) (RING- K1AA0714 1766 FALSE FALSE FALSE #N/A #N/A #N/A type E3 ubiquitin transferase Iisterin) (Zinc RNF160 finger protein 294) ZNF294 HSPC087

E3 ubiquitin-protein ligase makorin-1 (EC MKRN1 482 FALSE FALSE FALSE #N/A #N/A #N/A Q9UHC7 RNF61 3 2 ) ( G P te n ) R - ype E3 ubiquitin transferase makorin-1) E3 ubiquitin-protein ligase RAD18 (EC „ 2.3.2 27) (Postreplication repair protein Q9NS91 RNF73 FALSE FALSE FALSE #N/A #N/A #N/A

RNF14 ARA54 Q9UBS8 FALSE FALSE FALSE #N/A #N/A #N/A HRIHFB2 38

R Q149N8 23 FALSE FALSE FALSE #N/A #N/A #N/A

TRI 4 Q9C037Q c 7 FALSE FALSE TRUE #N/A #N/A #N/A RNF87 u qu n rans erase par e w motif-containing protein 4) o E3 ubiquitin-protein ligase UBR3 (EC 2.3.2.27) UBR3 (N-recognin-3) (RING-type E3 ubiquitin KIAA2024 transferase UBR3) (Ubiquitin-protein ligase E3- FALSE FALSE FALSE #N/A #N/A #N/A ZNF650 alpha-3) (Ubiquitin-protein ligase E3-alpha-ll!) (Zinc finger protein 650)

EGLN1 Eg nine hornolog 1 (EC 1.14.1 1.29) (Hypoxia- C1orf12 inducible factor prolyl hydroxylase 2) (HIF- PNAS- Q9GZT9 PH2) (H F-pro y hydroxylase 2) (HPH-2) 426 FALSE FALSE FALSE #N/A #N/A #N/A (Prolyl hydroxylase domain-containing protein PNAS- 2) (PHD2) (SM-20) 137

Q8N3D4 EHBP1 L 1 EH domain-binding protein 1-like protein 1 1523 FALSE FALSE FALSE #N/A #N/A #N/A EHD1 PAST EH domain-containing protein 1 (PAST Q9H4M9 PAST1 534 FALSE FALSE FALSE #N/A #N/A #N/A homo!og 1) (hPASTI) (Testilin) CDABP01 3 1 EHD2 EH domain-containing protein 2 (PAST Q9NZN4 543 FALSE FALSE FALSE #N/A #N/A #N/A PAST2 homo!og 2) EEF1A2 Elongation factor 1-alpha 2 (EF~1~alpha-2) EEF1AL (Eukaryotic elongation factor 1 A-2) (eEF1A-2) 463 FALSE FALSE FALSE #N/A #N/A #N/A STN (Statin-S1) Endonudease G , mitochondria! (Endo G) (EC ENDOG 297 FALSE FALSE FALSE #N/A #N/A #N/A 3.1 .30.-) Endophilin-A2 (EEN fusion partner of LL) SH3GL1 (Endophiiin-2) (Extra eleven-nineteen Q99961 CNSA1 leukemia fusion gene protein) (EEN) (SH3 368 FALSE FALSE FALSE #N/A #N/A #N/A SH3D2B domain proiein 2B) (SH3 domain-containing GRB2-iike protein 1) Enoyl-CoA delta isomerase 1, mitochondria! (EC 5.3.3.8) (3,2-trans-enoyl-CoA isomerase) ECU DC! (Deita(3),De!ta(2)-enoyl-CoA isomerase) 302 FALSE FALSE FALSE #N/A #N/A (D3,D2-enoy!~CoA isomerase) (Dodecenoy!- CoA isomerase) EPPK1 P58107 Epip!akin (450 kDa epidermal antigen) 5090 FALSE FALSE FALSE #N/A #N/A #N/A EPIPL GATA1 Eryfhroid transcription factor (Eryfl) (GAT A- P15976 ERYF1 binding factor 1) (GATA-1) (GF-1) (NF-E1 413 FALSE FALSE FALSE #N/A #N/A #N/A GF1 DNA-binding protein)

Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (CTP:phosphoethanolamine Q99447 PCYT2 389 FALSE FALSE FALSE #N/A #N/A #N/A cytidylyltransferase) (Phosphorylethanolamine transferase)

EXOC2 Exocyst complex component 2 (Exocyst Q96KP1 SEC5 924 FALSE FALSE FALSE #N/A #N/A #N/A complex component Sec5) S E C 5 L 1 EXOSC6 X SO ∞ m x componeni TR3 Q5RKV6 T 3 (Exosome component 6} (mRNA transport 272 FALSE FALSE FALSE #N/A #N/A #N/A regulator 3 homolog) (hMtr3) (p1 1)

EXOSC7 Exosome complex component RRP42 Q 15024 K AA0 16 (Exosome component 7) (Ribosoma! RNA- 291 FALSE FALSE FALSE #N/A #N/A #N/A processing protein 42) (p8) Exosome complex component RRP43 EXOSC8 (Exosome component 8) (Opa-interacting O IP2 276 FALSE FALSE FALSE #N/A #N/A #N/A protein 2) (OI P-2) (Ribosomal R A- RRP43 processing protein 43) (p9)

Exosome complex component RRP45 (Autoantigen PM/Scl 1) (Exosome component EXOSC9 polymyositis-scleroderma overlap Q06265 syndrome-associated autoantigen) 439 FALSE TRUE FALSE #N/A #N/A #N/A Vib L (polymyositis/scleroderma autoantigen 1 (Polymyositis/scleroderma autoantigen 75 kDa) (PM/Scl-75)

Exosome complex component RRP46 EXOSC5 (Chronic myelogenous leukemia tumor NQT4 CIV1L28 antigen 28) (Exosome component 5) 235 FALSE FALSE FALSE #N/A #N/A #N/A RRP46 (Ribosomal RNA-processing protein 46) (p1 2B)

DISS Exosome complex exonuclease RRP44 (EC 3Y2L1 K1AA1 0Q8 3 .1.13.-) (EC 3 .1.26.-) (Protein DISS homolog) 958 TRUE TRUE FALSE #N/A #N/A #N/A RRP44 (Ribosomal RNA-processing protein 44)

FAD synthase (EC 2 7.7.2) (FAD pyrophosphorylase) (F N j g FLAD1 adenylyltransferase) (Flavin adenine 587 FALSE FALSE FALSE #N/A #N/A #N/A PP591 dinucleotide synthase) [ Includes: Molybdenum cofactor biosynthesis protein-like region; FAD synthase region] FBX06 F-box only protein 6 (F-box protein that FBG2 Q9NRD1 recognizes sugar chains 2) (F-box/G-domain 293 FALSE FALSE FALSE #N/A #N/A #N/A FBS2 protein 2) FBX6 FH1/FH2 domain-containing protein 1 (Formin FHOD1 homolog overexpressed in spleen 1) (FHOS) Q9Y613 FHOS 1164 TRUE TRUE TRUE #N/A #N/A #N/A (Formin homology 2 domain-containing protein FHOS1 1) FLNC Filamin-C (FLN-C) (FLNc) (ABP-280-like Q14315 ABPL protein) (ABP-L) (Actin-binding-like protein) 2725 FALSE FALSE FALSE #N/A #N/A #N/A FLN2 (Filamin-2) (Gamrrsa-filamin)

Flavin reductase (NADPH) (FR) (EC 1.5.1 .30) (Biliverdin reductase B) (BVR-B) (EC 1.3.1 .24) BLVRB P30043 (Biliverdin-IX beta-reductase) (Green heme- 2 6 FALSE FALSE FALSE #N/A #N/A #N/A FLR binding protein) (GHBP) (NADPH-dependent diaphorase) (NADPH-flavin reductase) (FLR)

075955 FLOT1 Flotillin-1 427 TRUE FALSE FALSE #N/A #N/A #N/A •J\ FLOT2 Flotillin-2 (Epidermal surface antigen) (ESA) Q14254 ESA1 (Membrane component chromosome 17 428 FALSE FALSE FALSE #N/A #N/A #N/A M17S1 surface marker 1) FOXK1 Forkhead box protein K 1 (Myocyte nuclear P85037 733 FALSE FALSE FALSE #N/A #N/A #N/A MNF factor) (MNF)

FHL3 Four and a half LIM domains protein 3 (FHL-3) Q13643 280 FALSE FALSE FALSE #N/A #N/A #N/A SLIM2 (Skeletal muscle LIM-protein 2) (SLIM-2) Q9H479 FN3K Fructosamine-3-kinase (EC 2.7.1.-) 309 FALSE FALSE FALSE #N/A #N/A #N/A Fumarylaceioacetase (FAA) (EC 3.7.1.2) P16930 FAH (Beta-diketonase) (Fumarylacetoacetate 419 FALSE FALSE FALSE #N/A #N/A #N/A hydrolase) Galectin-1 (Ga - ) (14 kDa laminin-binding protein) (HLBP14) (14 kDa lectin) (Beta- ga!actoside-binding lectin L-14-1) (Galaptin) P09382 LGALS1 135 FALSE FALSE FALSE #N/A #N/A #N/A (HBL) (HPL) (Lactose-binding lectin 1) (Lectin galactoside-binding soluble 1) (Putative MAPK- activating protein PM12) (S-Lac lectin 1)

GTSF1 Gametocyte-specific factor 1 (Protein Q8WW33 167 FALSE FALSE FALSE #N/A #N/A #N/A FA 112B FA 112B) General transcription factor 3C polypeptide 5 GTF3C5 (TFSC-epsiion) (Transcription factor NIC 63 Q9Y5Q8 CDABPOO kDa subunit) (TFIIIC 63 kDa subunit) 519 FALSE TRUE FALSE #N/A #N/A #N/A 17 (TFIIIC63) (Transcription factor NC subunit epsilon)

GATB Glutamyl-tRNA(Gln) amidotransferase subunit PET1 12 B, mitochondrial (Glu-AdT subunit B) (EC 075879 557 FALSE FALSE FALSE #N/A #N/A #N/A PET1 12L 6.3.5 -) (Cytochrome c oxidase assembly HSPC199 factor PET1 12 homolog)

Glycerol-3-phosphate phosphatase (G3PP) (EC 3.1 .3.21) (Aspartate-based ubiquitous Mg(2+)~dependent phosphatase) (AUM) (EC 321 FALSE FALSE FALSE #N/A #N/A #N/A 3.1 .3.48) (Phosphoglycolate phosphatase) (PGP)

Glycogenin-1 (GN-1) (GN1) (EC 2.4.1 .186) 350 FALSE FALSE FALSE #N/A #N/A #N/A GYG (MN sialoglycoprotein) (PAS-2) P02724 ein alpha) (CD antigen 150 FALSE FALSE FALSE #N/A #N/A #N/A

GYPC Giycophorin-C (Giycoconnectin) (Giycophorin- P04921 GLPC D) (GPD) (Glycoprotein beta) (PAS-2') 128 FALSE FALSE FALSE #N/A #N/A #N/A GPC (Sialoglycoprotein D) (CD antigen CD236) Giycosylphosphafidylinositol anchor GPAA1 043292 attachment 1 protein (GPI anchor attachment 621 FALSE FALSE FALSE #N/A #N/A #N/A GAA1 protein 1) (GAA1 protein homolog) (hGAA1)

Go g reassembly-stacking protein 2 (GRS2) GORASP (Golgi phosphoprotein 6) (GOLPH6) (Golgi Q9H8Y8 2 452 FALSE TRUE TRUE #N/A #N/A #N/A reassembly-stacking protein of 55 kDa) GOLPH6 (GRASP55) (p59) GPi-anchor transamidase (GP transamidase) PICK (EC 3.-.-.-) (GPI8 homolog) (hGPIS) Q92643 395 FALSE FALSE FALSE #N/A #N/A #N/A GP 8 (Phosphatidyiinositol-glycan biosynthesis class K protein) (PIG-K)

GPN3 ATPBD1C AD-009 GPN-ioop GTPase 3 (ATP-binding domain 1 Q9UHW5 284 FALSE FALSE FALSE #N/A #N/A #N/A UNQ1876 family member C) /PR0431

GH T DERP2 Growth hormone-inducible transmembrane ICS 1 protein (Dermal papilla-derived protein 2) Q9H3K2 TIVIBiMS (Mitochondrial morphology and cristae 345 TRUE TRUE FALSE #N/A #N/A #N/A My021 structure 1) (MICS1) (Transmembrane BAX UNQ244/ inhibitor motif-containing protein 5) PR0281 Q9BX10 GTPBP2 GTP-binding protein 2 602 FALSE FALSE FALSE #N/A #N/A #N/A Guanine nucleotide exchange factor for Rab- Q8TBN0 RAB3IL1 3A (Rab-3A-inferacting-like protein 1) (RabSA- 382 FALSE FALSE FALSE #N/A #N/A #N/A inferacting-like protein 1) (Rabin3-like 1)

HD domain-containing protein 2 (Hepatitis C C6orf74 Q7Z4H3 virus NS5A-transactivated protein 2) (HCV 2 4 FALSE FALSE FALSE #N/A #N/A #N/A NS5ATP2 NS5A-transactivated protein 2) CGI-130 JPT2 Jupiter microtubule associated homoiog 2 Q9H910 C16orf34 (Hematological and neurological expressed 1- 190 FALSE FALSE FALSE #N/A #N/A #N/A HN1 L L 1 like protein) (HN1-like protein)

HE GN Hemogen (Erythroid differentiation-associated EDAG gene protein) (EDAG-1) (Hemopoietic gene Q9BXL5 NDR 484 FALSE FALSE FALSE #N/A #N/A #N/A protein) (Negative differentiation regulator PRO1037 protein) PRO1620

Hemoglobin subunit beta (Beta-globin) P68871 HBB (Hemoglobin beta chain) [Cleaved into: LVV- 147 FALSE FALSE FALSE #N/A #N/A #N/A hemorphin-7; Spinorphin] Hemoglobin subunit gamma-2 (Gamma-2- P89892 HBG2 globin) (Hb F Ggamma) (Hemoglobin gamma- 147 FALSE FALSE FALSE #N/A #N/A #N/A 2 chain) (Hemoglobin gamma~G chain) Hemoglobin subunit theta-1 (Hemoglobin P09105 HBQ1 142 FALSE FALSE FALSE #N/A #N/A #N/A theta-1 chain) (Theta-1 -globin) Hepatocyte growth factor-regulated tyrosine 014964 HGS HRS 777 FALSE FALSE FALSE #N/A #N/A #N/A kinase substrate (Hrs) (Protein pp1 10)

Hexokinase-2 (EC 2 7.1.1) (Hexokinase type P52789 HK2 917 FALSE TRUE TRUE #N/A #N/A #N/A ) (HK II) (Muscle form hexokinase) HMGB3 High mobility group protein B3 (High mobility 015347 HMG2A group protein 2a) (HMG-2a) (High mobility 200 FALSE FALSE FALSE #N/A #N/A #N/A HMG4 group protein 4) (HMG-4) HDAC6 Q9UBN7 KIAA0901 Histone deacetylase 6 (HD6) (EC 3.5. 1.98) 1215 FALSE FALSE FALSE #N/A #N/A #N/A J 2 1 H I9T1 H 1 P10412 " , ' ' Histone H 1.4 (Histone H1b) (Histone H1s-4) 219 FALSE FALSE FALSE #N/A #N/A #N/A b H 1r 4 K T2B HRX2 Histone-lysine N-methyltransferase 2B (Lysine KIAA03G4 N-methyltransferase 2B) (EC 2 1.1.43) Q9UMN6 MLL2 (Myeloid/lymphoid or mixed-lineage leukemia 2715 FALSE FALSE FALSE #N/A #N/A #N/A MLL4 protein 4) (Trithorax homolog 2) (WW domain- TRX2 binding protein 7) (WBP-7) WBP7

HIC2 Hypermethylated in cancer 2 protein (Hic-2) HRG22 (HIC1 -related gene on chromosome 22 Q96JB3 615 FALSE FALSE FALSE #N/A #N/A #N/A KIAA1020 protein) (Hic-3) (Zinc finger and BTB domain- ZBTB30 containing protein 30)

immunoglobulin heavy constant gamma 1 ( g gamma- 1 chain C region) (ig gamma-1 chain P01857 IGHG1 330 FALSE FALSE FALSE #N/A #N/A #N/A C region EU) (Ig gamma-1 chain C region KOL) (Ig gamma-1 chain C region N E)

Immunoglobulin heavy constant gamma 4 (Ig P01861 GHG4 327 FALSE FALSE FALSE #N/A #N/A #N/A garnma~4 chain C region) Immunoglobulin kappa constant (ig kappa chain C region) (ig kappa chain C region AG) (ig kappa chain C region CUM) (Ig kappa P01834 GKC 106 FALSE FALSE FALSE #N/A #N/A #N/A chain C region EU) ( g kappa chain C region OU) (Ig kappa chain C region ROY) (Ig kappa chain C region T )

IP01 1 lmportin-1 1 (imp1 1) (Ran-binding protein 1 ) Q9UI26 975 FALSE TRUE FALSE #N/A #N/A #N/A RANBP1 1 (RanBP1 1) Inosine triphosphate pyrophosphatase (ITPase) (Inosine triphosphatase) (EC 3 6.1.9) TPA (Non-canonical purine NTP pyrophosphatase) C20orf37 (Non-standard purine NTP pyrophosphatase) Q9BY32 y049 194 FALSE FALSE FALSE #N/A #N/A #N/A (Nucleoside-triphosphate diphosphatase) OK/SW- (Nucleoside-triphosphate pyrophosphatase) cl.9 (NTPase) (Putative oncogene protein hi 4-06 P) lnosine-5'-monophosphate dehydrogenase 1 1PDH1 ™ . ((IIMMPP ddeehhyyddrrooggeennaassee 11)) ( If P D 1) ( P D H 1) 514 FALSE FALSE FALSE #N/A #N/A #N/A VIr L 1 (EC 1 . 1 . 1 .205) (IMPDH-I)

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 PPIP5K2 (EC 2.7.4.21) (EC 2.7.4.24) (Diphosphoinositol HISPPD1 043314 pentakisphosphate kinase 2 ) (Histidine acid 1243 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0433 phosphatase domain-containing protein 1) V P2 (lnsP6 and PP-1P5 kinase 2 ) (VI P 1 homolog 2 ) (hsVIP2)

lnositoi-3-phosphate synthase 1 (IPS 1) (EC 5.5.1 .4) (Myo-inositoi 1-phosphate synthase) G9NPH2 558 FALSE FALSE FALSE #N/A #N/A #N/A (MI-1-P synthase) (MIP synthase) (h!PS) (Myo inositol 1-phosphate synthase A1) (hINOI) w Insulin-like growth factor 2 mRNA-binding ∞ IGF2BP2 protein 2 (IGF2 mRNA-binding protein 2 ) (I P- Q9Y6M1 P2 2 ) (Hepatocellular carcinoma autoantigen p62) 599 FALSE FALSE FALSE #N/A #N/A #N/A VICKZ2 ( G F- mRNA-binding protein 2 ) (VICKZ family member 2 ) Q14853 IRF3 Interferon regulatory factor 3 ( IRF-3) 427 FALSE FALSE FALSE #N/A #N/A #N/A

Interferon-induced, double-stranded RNA- activated protein kinase (EC 2.7.1 1 .1) (Eukaryotlc translation initiation factor 2-alpha E1F2AK2 kinase 2 ) (elF-2A protein kinase 2 ) (Interferon- P19525 PKR inducible RNA-dependent protein kinase) 551 FALSE FALSE FALSE #N/A #N/A #N/A PRKR (P1/elF-2A protein kinase) (Protein kinase RNA-activated) (PKR) (Protein kinase R) (Tyrosine-protein kinase EIF2AK2) (EC 2.7.10.2) (p68 kinase)

ISG20L2 Interferon-stimulated 2 0 kDa exonuclease-iike Q9H9L3 HSD-38 353 FALSE TRUE FALSE #N/A #N/A #N/A 2 (EC 3.1 .-.-) HSD38 n er eukin- receptor-associaied kinase 4 Q9NWZ3 (!RAK-4) (EC 2.7.1 1.1) (Renal carcinoma 460 FALSE FALSE FALSE #N/A #N/A #N/A antigen NY-REN-64) Q motif and SEC7 domain-containing protein IQSEC1 1 (ADP-ribosylation factors guanine nucleotide- ARFGEP exchange protein 0) (ADP-ribosylation Q6DN90 00 963 FALSE FALSE FALSE #N/A #N/A #N/A factors guanine nudeotide-exchange protein BRAG2 2) (Brefeldin-resistant Arf-GEF 2 protein) KIAA0763 (BRAG2)

Q96AB3 SOC2 Isochorismatase domain-containing protein 2 205 FALSE FALSE FALSE #N/A #N/A #N/A Jouberin (Abelson helper integration site 1 Q8N157 AHI1 1196 FALSE FALSE FALSE #N/A #N/A #N/A protein homolog) (AHI-1) Keratin, type cytoskeletal 23 (Cytokeratin-23) Q9C075 KRT23 422 FALSE FALSE FALSE #N/A #N/A #N/A (CK-23) (Keratin-23) (K23) Keratin, type II cytoskeletal 3 (65 kDa P12035 KRT3 cytokeratin) (Cytokeratin-3) (CK-3) (Keratin-3) 628 FALSE FALSE FALSE #N/A #N/A #N/A (K3) (Type-li keratin Kb3) KRT72 K6IRS2 Keratin, type II cytoskeletal 72 (Cytokeratin- KB35 72) (CK-72) (Kerafin-72) (K72) (Type II inner Q14CN4 5 11 FALSE FALSE FALSE #N/A #N/A #N/A KRT6 root sheath-specific keratin~K6irs2) (Type- 11 KRT6IRS keratin Kb35) 2 Kinesin heavy chain isoform 5A (Kinesin KIF5A Q12840 heavy chain neuron-specific 1) (Neuronal 1032 FALSE FALSE FALSE #N/A #N/A #N/A NKHC1 kinesin heavy chain) (NKHC) Kinetochore protein NDC80 homolog (Highly NDC80 expressed in cancer protein) (Kinetochore HEC 0 4777 protein He ) (HsHed) (Kinetochore- 642 FALSE FALSE FALSE #N/A #N/A #N/A HEC1 associated protein 2) (Retinoblastoma- KNTC2 associated protein HEC) KRR1 small subunit processome component KRR1 homolog (HIV-1 Rev-binding protein 2) (KRR- Q13601 381 TRUE FALSE FALSE #N/A #N/A #N/A HRB2 R motif-containing protein 1) (Rev-interacting protein 1) (Rip-1) La~re!ated protein 4Β (La ribonucleoprotein LARP4B domain family member 4B) (La Q92615 K1AAQ217 738 FALSE TRUE FALSE #N/A #N/A #N/A ribonucleoprotein domain family member 5) LARP5 (La-related protein 5)

LARP7 La-related protein 7 (La ribonucleoprotein Q4G0J3 HDCMA1 domain family member 7) (P-TEFb-interaction 582 FALSE FALSE FALSE #N/A #N/A #N/A 8P protein for 7SK stability) (PIP7S)

Q9H9A6 LRRC40 Leucine-rich repeat-containing protein 40 602 FALSE FALSE FALSE #N/A #N/A #N/A SERPINB Leukocyte elastase inhibitor (LEI) 1 (Monocyte/neutrophil elastase inhibitor) (E ) P30740 379 FALSE FALSE FALSE #N/A #N/A #N/A ELANH2 (M/NEI) (Peptidase inhibitor 2) (Pi-2) (Serpin NE PI2 B1) LIM and senescent cell antigen-like-containing LIMS1 domain protein 1 (Particularly interesting new P48059 PINCH 325 FALSE FALSE FALSE #N/A #N/A #N/A Cys-His protein 1) (PINCH-1) (Renal PINCH1 carcinoma antigen NY-REN-48)

ο A EA Macrophage erythrobiast attacher (Cell E P proliferation-inducing gene 5 protein) Q7L5Y9 396 FALSE FALSE FALSE #N/A #N/A # /A HLC10 (Erythrobiast macrophage protein) (Human PIGS lung cancer oncogene 10 protein) (HLC-10)

Major facilitator superfamily domain-containing FSD10 Q14728 protein 0 (Tetracycline transporter-like 455 FALSE FALSE FALSE #N/A #N/A #N/A TETRAN protein) Mannan-binding lectin serine protease 1 (EC 3.4.21.-) (Complement factor MASP-3) (Complement-activating component of Ra- reactive factor) (Mannose-binding lectin- 1ASP1 associated serine protease 1) (MASP-1) CRARF P48740 : (Mannose-binding protein-associated serine 699 FALSE FALSE FALSE #N/A #N/A #N/A CRARF1 protease) (Ra-reactive factor serine protease PRSS5 p100) (RaRF) (Serine protease 5) [Cleaved into: Mannan-binding lectin serine protease 1 heavy chain; Mannan-binding lectin serine protease 1 light chain]

Melanoma antigen preferentially expressed in PRA E tumors (Opa-interacting protein 4) (OIP-4) MAPE 509 FALSE TRUE TRUE #N/A #N/A #N/A (Preferentially expressed antigen of melanoma)

Melanoma-associated antigen B2 (Cancer/testis antigen 3.2) (CT3.2) (DSS-AHC 0 15479 MAGEB2 319 FALSE FALSE FALSE #N/A #N/A #N/A critical interval MAGE superfamily 6) (DAM6) (MAGE XP-2 antigen) (MAGE-B2 antigen)

Melanoma-associated antigen C 1 060732 MAG EC 1 (Cancer/testis antigen 7.1) (CT7.1) (MAGE-C1 1142 FALSE FALSE FALSE #N/A #N/A #N/A antigen) Membrane-associated tyrosine- and threonine- Q99640 - specific cdc2-inhibitory kinase (EC 2.7.1 1.1) 499 FALSE FALSE FALSE #N/A #N/A #N/A (Myt1 kinase)

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial (MCCase subunit beta) (EC 1CCC2 6.4. .4) (3-methylcrotonyl-CoA carboxylase 2) Q9HCC0 563 FALSE FALSE FALSE #N/A #N/A #N/A ICC B (3-methylcrotonyi-CoA carboxylase non-biotin- containing subunit) (S-metbyicrotonyl- CoA:carbon dioxide ligase subunit beta)

Methylenetetrahydrofolate reductase (EC T HFR 656 FALSE FALSE FALSE #N/A #N/A #N/A 1.5.1 .20) Meihylosome subunit pICIn (Chloride channel CLNS1A nucleotide sensitive 1A) (Chloride P54105 CLCI conductance regulatory protein ICIn) (l(Cln)) 237 FALSE FALSE FALSE #N/A #N/A #N/A C L N (Chloride ion current inducer protein) (C ) (Reticulocyte pICIn)

p p rr \ *hylthioribulose~1 -phosphate dehydratase Q96GX9 2 (MTRu-1-P dehydratase) (EC 4.2.1 .109) 242 FALSE FALSE FALSE #N/A #N/A #N/A (APAF1 -interacting protein) (hAPIP)

ET T L7 A PRO0066 Methyltransferase-like protein 7A (EC 2.1 . 1 .-) UNQ1902 244 FALSE FALSE FALSE #N/A #N/A #N/A (Protein AAM-B) /PR0434

IC13 COS complex subunit MIC13 (Protein Q5XKP0 C19orf7Q 1 18 FALSE FALSE FALSE #N/A #N/A #N/A QIL1 Microsomal glutathione S-transferasc IG S T 2 5735 (Microsomal GST-2) (EC 2.5.1 .18) 147 FALSE FALSE FALSE #N/A #N/A #N/A GST2 (Microsomal GST-ii) Microtubuie-associated protein 1 B (MAP-1 B) P46821 MAPI B [Cleaved into: MAPI B heavy chain; MAPI 2468 FALSE FALSE FALSE #N/A #N/A #N/A light chain LC1] SLC25A2 Mitochondrial 2-oxodicarboxylate carrier 299 FALSE FALSE FALSE #N/A #N/A #N/A 1 ODC (Solute carrier family 2 5 member 21) FIS1 Mitochondrial fission 1 protein (FIS1 homolog) Q9Y3D6 TTC1 1 (hFisl) (Tetratricopeptide repeat protein 1 ) 152 FALSE FALSE FALSE #N/A #N/A #N/A CG!-135 (TPR repeat protein 1 1) MGME1 Mitochondrial genome maintenance B Q P 7 C20orf72 344 FALSE FALSE FALSE #N/A #N/A #N/A exonuclease 1 (EC 3.1.-.-) DDK1 !itochondriai glutamate carrier 1 (GC-1) S:LLCC2255AA2 5H936 . (G3lluuttaammaattee//HH((++)) ssyymmppoi rter 1) (Solute carrier 323 FALSE FALSE FALSE #N/A #N/A #N/A 2 GC1 family 2 5 member 22) Mitochondrial inner membrane protein OXA1 L Q15070 OXA1 L (Hsa) (OXA1 Hs) (Oxidase assembly 1-like 435 TRUE FALSE FALSE #N/A #N/A #N/A protein) (OXA1-like protein)

MPC1 BRP44L CG - 29 Mitochondrial pyruvate carrier 1 (Brain protein Q9Y5U8 109 FALSE FALSE FALSE #N/A #N/A #N/A HSPC040 44-like protein) PNAS- 115 MFN2 Mitofusin-2 (EC 3.6.5.-) (Transmembrane 095140 CPRP1 757 FALSE FALSE FALSE #N/A #N/A #N/A GTPase MFN2) KIAA0214

Mitogen-activated protein kinase 1 (MAP MAPK1 kinase 1) (MARK 1) (EC 2.7.1 1.24) (ERT1) (Extracellular signal-regulated kinase 2) (ERK- P28482 360 TRUE FALSE FALSE #N/A #N/A #N/A PR 2) (MAP kinase isoform p42) (p42-MAPK) PR (Mitogen-activated protein kinase 2) (MAP kinase 2) (MAPK 2)

Mothers against decapentapiegic homo!og 4 S AD4 (MAD homolog 4) (Mothers against DPP Q13485 DPC4 homolog 4) (Deletion target in pancreatic 552 FALSE FALSE FALSE #N/A #N/A #N/A MADH4 carcinoma 4) (SMAD family member 4) (SMAD 4) (Smad4) (hSMAD4) Multidrug resistance-associated protein 4 (ATP-binding cassette sub-family C member ABCC4 O15439 4) (MRP/cMOAT-reiated ABC transporter) 1325 FALSE FALSE FALSE #N/A #N/A #N/A MRP4 (Multi-specific organic anion transporter B) (MOAT-B) MYL4 Myosin light chain 4 (Myosin light chain 1, P12829 MLC1 embryonic muscle/atriai isoform) (Myosin light 197 FALSE FALSE FALSE #N/A #N/A #N/A PR01957 chain alkali GT-1 isoform) Myosin light chain kinase, smooth muscle 1YLK ( LCK) (smMLCK) (EC 2.7.1 .18) (Kinase- MLCK Q15746 related protein) (KRP) (Teiokin) [Cleaved into: 1914 FALSE FALSE FALSE #N/A #N/A #N/A 1LCK1 Myosin light chain kinase, smooth muscle, MYLK1 deglLftamylated form] NLRP2 NACHT, LRR and PYD domains-containing NALP2 protein 2 (Nucleotide-binding site protein 1) G9NX02 NBS1 (PYRIN domain and NACHT domain- 1062 FALSE FALSE FALSE #N/A #N/A #N/A PAN1 containing protein 1) (PYRIN-containing PYPAF2 APAF1 -like protein 2)

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (Cell death regulatory NDUFA13 protein GRIM-19) (Complex I-B16.6) (Cl- GRI 19 B16.6) (Gene associated with retinoic and Q9P0J0 144 FALSE TRUE FALSE #N/A #N/A #N/A CDA016 interferon-induced mortality 19 protein) (GRIM CGI-39 19) (Gene associated with retinoic and IFN- induced mortality 19 protein) (NADH- ubiquinone oxidoreductase B16.6 subunit)

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (Complex l-PDSW) (C 096000 NDUFB10 172 FALSE FALSE FALSE #N/A #N/A #N/A PDSW) (NADH-ubiquinone oxidoreductase PDSW subunit) NADH dehydrogenase [ubiquinone] 1 beta NDUFB1 1 subcomplex subunit 11, mitochondrial Q9NX14 UNQ1 11/ (Complex l-ESSS) (CI-ESSS) (NADH- 153 FALSE FALSE FALSE #N/A #N/A #N/A PRO1064 ubiquinone oxidoreductase ESSS subunit) (Neuronal protein 17.3) (Np17.3) (p17.3) NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 , mitochondrial 186 FALSE FALSE FALSE #N/A #N/A #N/A (Complex l-ASHI) (CI-ASHI) (NADH- ubiquinone oxidoreductase ASHI subunit) NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 1.6 .5 3) (EC NDUFV1 P49821 1.6.99.3) (Complex 1-51 kD) (CI-51kD) (NADH 464 FALSE FALSE FALSE #N/A #N/A #N/A UQOR1 dehydrogenase flavoprotein 1) (NADH- ubiquinone oxidoreductase 5 1 kDa subunit)

NADPH:adrenodoxin oxidoreductase, mitochondrial (AR) (Adrenodoxin reductase) P22570 491 FALSE FALSE FALSE #N/A #N/A #N/A (EC 1.18.1 .6) (Ferredoxin-NADP(+) reductase) (Ferredoxin reductase)

NEDD8 (Neddyiin) (Neural precursor cell expressed deveiopmentaliy down-regulated Q 15843 NEDDS 8 1 FALSE FALSE FALSE #N/A #N/A #N/A protein 8) (NEDD-8) (Ubiquitin-like protein NeddS) NEDD8 ultimate buster 1 (Negative regulator NUB1 Q9Y5A7 of ubiquitin-like proteins 1) (Renal carcinoma 615 FALSE FALSE FALSE #N/A #N/A #N/A NYREN18 antigen NY-REN-18)

•J\ NCDN Q9UBB6 Neurochondrin 729 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0607

Neutral amino acid transporter A SLC1A4 (Alanine/serine/cysteine/threonine transporter P43007 ASCT1 532 FALSE FALSE FALSE #N/A #N/A #N/A ΐ) (ASCT-1) (SATT) (Solute carrier family 1 SATT member 4)

SLC1A5 Neutral amino acid transporter B(0) (ATB(O)) ASCT2 (Baboon 7 virus receptor) (RD1 14/simian Q 15758 7V 1 type D retrovirus receptor) (Sodium-dependent 541 FALSE FALSE FALSE #N/A #N/A #N/A neutral amino acid transporter type 2) (Solute carrier family 1 member 5)

Q8N5F7 NKAP NF-kappa-B-activating protein 415 FALSE FALSE FALSE #N/A #N/A #N/A NKRF NF-kappa-B-repressing factor (NFkB- O 15226 ITBA4 repressing factor) (Protein ITBA4) 690 FALSE FALSE FALSE #N/A #N/A #N/A NRF (Transcription factor NRF) Niban-like protein 1 (Meg~3) (Melanoma FAM129E Q96TA1 invasion by ERK) (MINERVA) (Protein 746 FALSE FALSE FALSE #N/A #N/A #N/A C9orf88 FAM129B) Nicotinate-nucleotide pyrophosphatase [carboxylating] (EC 2.4.2 19) (Quinolinate Q15274 QPRT 297 FALSE FALSE FALSE #N/A #N/A #N/A phosphoribosyltransferase [decarboxylating]) (QAPRTase) (QPRTase) ΝΟΜ0 1 015155 Nodal modLflator 1 (pM5 protein) 1222 FALSE TRUE FALSE #N/A #N/A #N/A Ρ 5 Non-canonical poiy(A) RNA polymerase PAPD5 (EC 2.7.7.19) (PAP-associated domain-containing protein 5) (Terminal Q8NDF8 PAPD5 572 FALSE FALSE FALSE #N/A #N/A #N/A uridylyltransferase 3) (TUTase 3) (Topoisomerase-related function protein 4-2) (TRF4-2) Nostrin (B 247 homolog) (Nitric oxide Q8M9 NOSTRIN synthase traffic inducer) (Nitric oxide synthase 5 6 FALSE FALSE FALSE #N/A #N/A #N/A trafficker) (eNOS-trafficking inducer) NEMF Nuclear export mediator factor NEMF (Antigen 060524 SDCCAG NY-CO-1) (Serologically defined colon cancer 1076 FALSE FALSE FALSE #N/A #N/A #N/A 1 antigen 1) NRBF2 Nuclear receptor-binding factor 2 (NRBF-2) Q96F24 287 FALSE FALSE FALSE #N/A #N/A #N/A COPR (Comodulator of PPAR and RXR) NUCKS1 Nuclear ubiquitous casein and cyclin- Q9H1 E3 NUCKS 243 FALSE FALSE FALSE #N/A #N/A #N/A dependent kinase substrate 1 (P1) JC7 Nuclear-interacting partner of ALK (Nuclear- ZC3HC1 interacting partner of anaplastic lymphoma Q86WB0 N PA 502 TRUE FALSE FALSE #N/A #N/A #N/A kinase) (hNIPA) (Zinc finger C3HC-type HSPC216 protein 1) GNL2 Nucleolar GTP-binding protein 2 (Autoantigen Q13823 731 FALSE FALSE FALSE #N/A #N/A #N/A NGP1 NGP-1) NOP14 C4orf9 Nucleolar protein 14 (Nucleolar complex P78316 857 FALSE FALSE FALSE #N/A #N/A #N/A NOL14 protein 14) RES4-25

ZCCHC17 Nucleolar protein of 40 kDa (pNO40) (Pnn- PS1 D interacting nucleolar protein) (Putative S 1 Q9NP64 HSPC243 RNA-binding domain protein) (PS1 protein) 241 FALSE FALSE FALSE #N/A #N/A #N/A HSPC251 (Zinc finger CCHC domain-containing protein LDC4 17)

GLE1 Nucieoporin GLE1 (hGLE1) (GLE1-iike Q53GS7 698 FALSE FALSE FALSE #N/A #N/A #N/A GLE1 L protein) O-acety!-ADP-ribose deacefylase MACROD1 MACROD (EC 3.2.2.-) (EC 3.5.1 .-) (MACRO domain- Q9BQ69 325 FALSE FALSE FALSE #N/A #N/A #N/A 1 LRP16 containing protein 1) (Protein LRP16) ([Protein ADP~ribosylglutamate] hydrolase)

5 Oligoribonuclease, mitochondrial (EC 3.1 .-.-) Q9Y3B8 - . (RNA exonuclease 2 homolog) (Small 237 FALSE FALSE FALSE #N/A #N/A #N/A SMFN Q I fragment nuclease) Ornithine aminotransferase, mitochondrial (EC 2.6.1 .13) (Ornithine delta-aminotransferase) (Ornithine-oxo-acid aminotransferase) P04181 OAT 439 FALSE FALSE FALSE #N/A #N/A #N/A [Cleaved into: Ornithine aminotransferase, hepatic form; Ornithine aminotransferase, renai form] Oxygen-dependent coproporphyrinogen-IH CPOX oxidase, mitochondrial (COX) (Coprogen P36551 454 FALSE FALSE FALSE #N/A #N/A #N/A CPO CPX oxidase) (Coproporphynnogenase) (EC 1.3.3.3) OSBPL3 K1AA0704 Oxysterol-binding protein-related protein 3 Q9H4L5 887 FALSE FALSE FALSE #N/A #N/A #N/A ORP3 (ORP-3) (OSBP-related protein 3) OSBP3 OSBPL9 Oxysterol-binding protein-related protein 9 Q96SU4 736 TRUE TRUE FALSE #N/A #N/A #N/A (ORP-9) (OSBP-related protein 9} OSBP4 PDLI 1 PDZ and L domain protein 1 (C-terminal 000151 CLIM1 LIM domain protein 1) (Elfin) (LIM domain 329 FALSE FALSE FALSE #N/A #N/A #N/A CLP36 protein CLP-36) PDLIM5 domain protein 5 (Enigma Q96HC4 homolog) (Enigma-like PDZ and LIM domains 596 FALSE FALSE FALSE #N/A #N/A #N/A ENH L9 protein)

PDLI 7 PDZ and LIM domain protein 7 (LIM Q9NR12 457 FALSE FALSE FALSE #N/A #N/A #N/A ENIGMA mineralization protein) (LMP) (Protein enigma)

Peptide-N(4)-(N-acetyl-beta- NGLY1 glucosaminyi)asparagine amidase (PNGase) Q96 V 654 FALSE F L FALSE! #N/A #N/A #N/A PNG1 (hPNGase) (EC 3.5.1 .52) (N-glycanase 1) (Peptide: N-glycanase)

Peroxisome biogenesis factor 1 (Peroxin-1) 043933 PEX1 1283 FALSE FALSE FALSE #N/A #N/A #N/A (Peroxisome biogenesis disorder protein 1) oe PI4KA Phosphatidylinositol 4-kinase alpha (PI4- P42356 PIK4 kinase alpha) (PI4K-alpha) (Ptdlns-4-kinase 2102 FALSE FALSE FALSE #N/A #N/A #N/A PIK4CA alpha) (EC 2.7.1 .67) Phosphoacetylglucosamine mutase (PAGM) PGM3 2 (A y c s m 095394 phosphomutase) (N-acetylglucosamine- 542 FALSE FALSE FALSE #N/A #N/A #N/A G? phosphate mutase) (Phosphoglucomutase-3) (PGM 3)

PCK2 Phosphoenolpyruvate carboxykinase [GTP], Q 16822 640 FALSE FALSE! #N/A #N/A #N/A PEPCK2 mitochondrial (PEPCK-M) (EC 4 .1.1.32)

Phosphoiipase D3 (PLD 3) (EC 3.1.4.4) PLD3 ( oline phosphatase 3) (Hindi! I K4L 490 FALSE FALSE FALSE #N/A #N/A # /A homolog) (Hu-K4) (Phosphatidylcholine- hydrolyzing phosphoiipase D3) PITHD1 C1orf128 Q9GZP4 AD039 P T H domain-containing protein 1 2 11 FALSE FALSE FALSE #N/A #N/A #N/A ΗΤ0 4 ΡΡ603

Plasma membrane calcium-transporting ΑΤΡ2 Β1 ATPase 1 (PMCA1) (EC 3.6.3.8) (Plasma 1258 FALSE FALSE FALSE #N/A #N/A #N/A Ρ membrane calcium ATPase isoform 1) (Plasma membrane calcium pump isoform 1)

Poiyadenyiate-binding protein-interacting protein 1 (PABP-interacting protein 1) {PAIP- Q9H074 ΡΑΙΡ1 479 FALSE FALSE FALSE #N/A #N/A #N/A 1) (Poly(A)-binding protein-interacting protein 1) CAVIN1 Caveolae-associated protein 1 (Cavin-1) Q6 Z 2 PTRF 390 TRUE TRUE FALSE #N/A #N/A #N/A (Polymerase and transcript release factor) FKSG13 ΡΤΒΡ 3 Polypyrimidine tract-binding protein 3 095758 552 FALSE FALSE FALSE #N/A #N/A #N/A ROD1 (Regulator of differentiation 1) (Rod1) HIV3BS Porphobilinogen deaminase (PBG-D) (EC Ρ08397 PBGD 2.5.1 .61) (Hydroxymethylbilane synthase) 361 FALSE FALSE FALSE #N/A #N/A #N/A UPS (HMBS) (Pre-uroporphyrinogen synthase) P0CG39 POTEJ POTE ankyrin domain family member J 1038 FALSE FALSE FALSE #N/A #N/A #N/A Prelamin-A/C [Cleaved into: Lamin-A/C (70 L A Ρ02545 kDa !amin) (Renal carcinoma antigen NY-REN- 664 FALSE FALSE FALSE #N/A #N/A #N/A L N1 32)] Pre-mRNA-splicing factor 38B (Sarcoma Q5VTL8 PRPF38B 546 FALSE FALSE FALSE #N/A #N/A #N/A antigen NY-SAR-27) DHX38 Pre-mRNA-splicing factor ATP-dependent DDX38 RNA helicase PRP16 (EC 3.6.4.13) (ATP- Q92620 1227 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0224 dependent RNA helicase DHX38) (DEAH box PRP16 protein 38) NSUN5 , η Λ , . NSUN5A r RNA (cytosine-C(5))- methyliransferase (EC 2.1 1 .-) (NOL1 -related Q96P1 1 P ) (N O L R ) (NOL1/NOP2/Sun domain 429 FALSE FALSE FALSE #N/A #N/A #N/A family member 5) (Wiiliams-Beuren syndrome , . chromosomal region 20A proiesn)

Probable ATP-dependent RNA helicase Q9H6S0 YTHDC2 YTHDC2 (EC 3.6.4.13) (YTH domain- 1430 FALSE FALSE FALSE #N/A #N/A #N/A containing protein 2) COLGAL Procollagen galactosyltransferase 1 (EC T 1 2.4.1 .50) (Collagen beta(1- Q8NBJ5 GLT25D1 0)galactosyltransferase 1) 622 FALSE FALSE FALSE #N/A #N/A #N/A PSECQ24 (Glycosyltransferase 25 family member 1) 1 (Hydroxylysine galactosyltransferase 1)

Procollagen-lysine, 2-oxoglutarate 5- 060568 PLOD3 dioxygenase 3 (EC 1.14.1 1.4) (Lysyl 738 FALSE FALSE FALSE #N/A #N/A #N/A w hydroxylase 3) (LH3) ° PDCD2 Programmed cell death protein 2 (Zinc finger Q16342 RP8 YND domain-containing protein 7) (Zinc 344 TRUE FALSE FALSE #N/A #N/A #N/A ZMYND7 finger protein Rp-8) P3H1 GROS1 Prolyl 3-hydroxylase 1 (EC 1.14.1 1.7) (Growth Q32P28 LEPRE1 suppressor 1) (Leucine- and proline-enriched 736 FALSE FALSE FALSE #N/A #N/A #N/A PSEC010 proteoglycan 1) (Leprecan-1) 9

Prosaposin (Proacfivator polypeptide) [Cleaved into: Saposin-A (Protein A); Saposin- B-Val; Saposin-B (Cerebroside sulfate PSAP activator) (CSAct) (Dispersin) (Sphingoiipid 32 GLBA activator protein 1) (SAP-1) (Sulfatide/GM1 524 FALSE FALSE FALSE #N/A #N/A #N/A SAP1 activator); Saposin-C (A1 activator) (Co-beta- glucosidase) (Glucosyiceramidase activator) (Sphingoiipid activator protein 2) (SAP-2); Saposin-D (Component C) (Protein C)] Prostaglandin reductase 2 (PRG-2) (EC PTGR2 1.3.1 .48) (15-oxoprostaglandin 13~reductase) Q8N8N7 351 FALSE FALSE FALSE #N/A #N/A #N/A ZADH1 (Zinc-binding alcohol dehydrogenase domain- containing protein 1)

PS E4 Proteasome activator complex subunit 4 Q14997 1843 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0077 (Proteasome activator PA200)

PS G2 Proteasome assembly chaperone 2 (PAC-2 HCCA3 (Hepatocellular carcinoma-susceptibility Q969U7 PAC2 264 FALSE FALSE FALSE #N/A #N/A #N/A protein 3) (Tumor necrosis factor superfami TNFSF5 member 5-induced protein 1) P 1 EC 29 Proteasome-associated protein EC 29 Q5VYK3 1845 TRUE TRUE FALSE #N/A #N/A #N/A (IAA0368 homoiog (Ecm29)

AATF CHE1 Protein AATF (Apoptosis-antagonizing Q9NY61 transcription factor) (Rb-binding protein Che- 560 TRUE FALSE FALSE #N/A #N/A # /A DED HSPC277 1) Protein arginine N~methyitransferase 3 (EC PR T3 2.1 . 1 .-) (Heterogeneous nuclear 060678 531 TRUE FALSE FALSE #N/A #N/A #N/A HR T L3 ribonucleoprotein methyitransferase-like protein 3) Protein argonaute-2 (Argonaute2) (hAgo2) AG02 n (A ° R S catalytic Q9UKV8 component 2) (Eukaryotic translation initiation 859 FALSE FALSE FALSE #N/A #N/A #N/A EIF2C2 factor 2C 2) (elF-2C 2) (elF2C 2) (PAZ Piwi domain protein) (PPD) (Protein slicer) CNPY2 MSAP T E 4 Protein canopy homolog 2 (M!R-interacting Q9Y2B0 ZSIG9 saposin-like protein) (Putative secreted prote 182 FALSE TRUE FALSE #N/A #N/A #N/A UNQ1943 Zsig9) (Transmembrane protein 4) /PR0442

FAM207A Q9NSI2 C21orf70 Protein FA 2Q7A 230 TRUE FALSE FALSE #N/A #N/A #N/A PRED56

HEX 1 Protein HEXIM1 (Cardiac lineage protein 1) CLP1 (Estrogen down-regulated gene 1 protein) 094992 EDG1 359 FALSE FALSE FALSE #N/A #N/A #N/A (Hexametbylene bis-acetamide-inducible HIS1 protein 1) (Menage a quatre protein 1) AQ 1 KT 2 Q96EK9 Protein KTM2 homolog 354 FALSE FALSE FALSE #N/A #N/A #N/A SBBI81 LIN28B Q6Z 7 Protein lin-28 homolog B (Lin-28B) 250 FALSE FALSE FALSE #N/A #N/A #N/A CSDD2 LTV1 Q96GA3 Protein LTV1 homolog 475 FALSE FALSE FALSE #N/A #N/A #N/A C6orf93 LNP Q9C0E8 Protein lunapark 428 FALSE TRUE FALSE #N/A #N/A #N/A K AA 7 5

P39210 Protein Mpv17 176 FALSE FALSE FALSE #N/A #N/A #N/A FAM129A C1orf24 Protein Niban (Cell growth-inhibiting gene 3 Q9BZQ8 928 FALSE FALSE FALSE #N/A #N/A #N/A N BAN protein) (Protein FAM129A) GIG39 Protein O-GicNAcase (OGA) (EC 3.2.1 .169) (Beta-N-acetyiglucosarninidase) (EC 3.2.1 .-) GEA5 (Beta~N~aceiyibexosaminidase) (Beta- HEXC hexosaminidase) (Meningioma-expressed 060502 916 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0679 antigen 5) (N-acetyi-beta-D-glucosaminidase) EA5 (N-acetyl-beta-glucosaminidase) (Nuclear cytoplasmic O-GlcNAcase and aceiyltransferase) (NCOAT)

Protein POF1 B (Premature ovarian failure Q8WW4 POF1 B 589 FALSE FALSE FALSE #N/A #N/A #N/A protein 1B) Protein PRRC2A (HLA-B-associafed transcript PRRC2A 2) (Large proiine-rich protein BAT2) (Proline- P48634 2157 FALSE FALSE FALSE #N/A #N/A #N/A BAT2 G2 rich and coiied-coil-containing protein 2A) (Protein G2) Q96PU8 QK! HKQ Protein quaking (Hqk) (Hqkl) 341 FALSE TRUE FALSE #N/A #N/A #N/A Protein S100-A1 1 (Ca!gizzarin) (Metastatic S100A1 1 iymph node gene 7 protein) (MLN 70) P31949 MLN70 (Protein S100-C) (S100 calcium-binding 105 FALSE FALSE FALSE #N/A #N/A #N/A S100C protein A 11) [Cleaved into: Protein S100-A1 1 N-terminally processed]

TSA305 Protein sel~1 homolog 1 (Suppressor of lin-1 2- Q9UBV2 794 FALSE FALSE FALSE #N/A #N/A #N/A UNQ128/ like protein 1) (Se ) PR0 1063

Protein SET (HLA-DR-associated protein I) (Inhibitor of granzyme A-activated DNase) Q01 105 SET (IGAAD) (ΡΗΑΡΠ) (Phosphatase 2A inhibitor 290 FALSE FALSE FALSE #N/A #N/A #N/A I2PP2A) (I-2PP2A) (Template-activating factor ) (TAF-i)

Protein SSX1 (Cancer/testis antigen 5.1) 016384 SSX1 188 FALSE FALSE FALSE #N/A #N/A #N/A (CT5.1) (Synovial sarcoma, X breakpoint 1) SSX2 Protein SSX2 (Cancer/testis antigen 5.2) Q16385 SSX2A; (CT5.2) (Synovia! sarcoma, X breakpoint 2) 188 TRUE TRUE FALSE #N/A #N/A #N/A SSX2B (Tumor antigen HOM-MEL-40) Q92734 TFG Protein TFG (TRK-fused gene protein) 400 FALSE FALSE FALSE #N/A #N/A #N/A Protein transport protein Sec24A (SEC24- 095486 SEC24A 1093 FALSE FALSE FALSE #N/A #N/A #N/A re!ated protein A) Protein-glutamine gamma-glutamyltransferase 2 (EC 2 3.2. 3) (Tissue transglutaminase) P21980 TGM2 (Transglutaminase C) (TG(C)) (TGC) (TGase 687 FALSE FALSE FALSE #N/A #N/A #N/A C) (Transglutaminase H) (TGase H) (Transglutaminase-2) (TGase-2)

Protein-glutamine gamma-glutamyltransferase E (EC 2.3.2 3) (Transglutaminase E) (TG(E)) (TGE) (TGase E) (Transg!utaminase-3) (TGase-3) [Cleaved into: Protein-glutamine TG 3 693 FALSE FALSE FALSE #N/A #N/A #N/A gamma-glutamyltransferase E 50 kDa catalytic chain; Protein-glutamine gamma- glutamyltransferase E 27 kDa non-catalytic chain]

Protoporphyrinogen oxidase (PPO) (EC P50336 PPOX 477 FALSE FALSE FALSE #N/A #N/A #N/A 1.3.3.4) PUS7 Pseudouridyiate synthase 7 homoiog (EC Q96PZ0 661 TRUE FALSE FALSE #N/A #N/A #N/A KIAA1897 5.4.99 -)

HSP90AA Putative heat shock protein HSP 90-alpha A4 4P (Heat shock 90 kDa protein 1 alpha-like 2) Q58FG1 418 FALSE FALSE FALSE #N/A #N/A #N/A HSP90AD (Heat shock protein 90-alpha D) (Heat shock HSPCAL2 protein 90Ad)

HIST2H2 Putative histone H2B type 2-C (Histone H2B.t) Q6DN03 193 FALSE FALSE FALSE #N/A #N/A #N/A BC (Η2Β/Ϊ) ZNF66 Putative zinc finger protein 66 (Zinc finger Q6ZN08 573 FALSE FALSE FALSE #N/A #N/A #N/A ZNF66P protein 66 pseudogene) PDXK C21orf12 4 Pyridoxal kinase (EC 2.7 1.35) (Pyridoxine 000764 312 FALSE FALSE FALSE #N/A #N/A #N/A C21orf97 kinase) PKH PNK PRED79

Pyroglutamyl-peptidase 1 (EC 3.4 19.3) (5- oxopro!y!-peptidase) (Pyroglutamyl PGPEP1 Q9NXJ5 „ aminopeptidase !) (PAP-!) (Pyrogiutarnyl- 209 FALSE FALSE FALSE #N/A #N/A #N/A peptidase ) (PGP-I) (Pyrrolidone-carboxyiate peptidase) RAB1 1F! Rab1 1 family-interacting protein 1 (Rab1 1- Q6WKZ4 1283 FALSE FALSE FALSE #N/A #N/A #N/A P 1 RCP FIP1) (Rab-coupling protein) Q5HYI8 RABL3 Rab-like protein 3 236 FALSE FALSE FALSE #N/A #N/A #N/A Raguiator complex protein LAMTOR1 (Late LAMTOR endosomal/lysosomal adaptor and MAPK and 1 w MTOR activator 1) (Lipid raft adaptor protein ¾ Q6IAA8 C 11orf59 . . 161 FALSE FALSE FALSE #N/A #N/A #N/A ) (Protesn associated with- DR- s and PDRO endosornes) (p27Kip1 -releasing factor from PP7157 RhoA) (p27RF-Rho) RAB13 Ras-related protein Rab-13 (Cell growth- P51 153 203 FALSE FALSE FALSE #N/A #N/A #N/A G G4 inhibiting gene 4 protein) RAB27A Ras-related protein Rab-27A (Rab-27) (GTP- P51 159 221 FALSE FALSE FALSE #N/A #N/A #N/A RAB27 binding protein Ram) RAB31 Ras-related protein Rab-31 (Ras-related Q13636 194 FALSE FALSE FALSE #N/A #N/A #N/A RAB22B protein Rab-22B) REEP5 Receptor expression-enhancing protein 5 Q00765 C5orf18 189 FALSE FALSE FALSE #N/A #N/A # /A (Polyposis locus protein 1) (Protein TB2) DP1 TB2 REEP6 Receptor expression-enhancing protein 6 Q96HR9 C19orf32 184 FALSE FALSE FALSE #N/A #N/A #N/A (Polyposis locus protein 1-like 1) DP1 L 1 Receptor-type tyrosine-protein phosphatase PTPRB beta (Protein-tyrosine phosphatase beta) (R- P23467 1997 FALSE FALSE FALSE #N/A #N/A #N/A PTPB PTP-beta) (EC 3 . 3.48) (Vascular endothelial protein tyrosine phosphatase) (VE-PTP)

Reticulon-3 (Homolog of ASY protein) (HAP) RTN3 (Neuroendocrine-specific protein-like 2) (NSP- ASYIP 1Q32 FALSE TRUE FALSE #N/A #N/A #N/A ike protein 2) (Neuroendocrine-specific NSPL2 protein-like II) ( SP- ike protein II) (NSPLII)

Retinal dehydrogenase 2 (RALDH 2) (Ra!DH2) (EC 1.2.1 .36) (Aldehyde ALDH1A2 dehydrogenase family 1 member A2) 518 FALSE FALSE FALSE #N/A #N/A #N/A RALDH2 (Retinaldehyde-specific dehydrogenase type 2) (RALDH(II))

RDH13 3 PSEC008 d yd ° s 1. 1 --) (Short chain dehydrogenase/reductase family 7C 331 FALSE FALSE FALSE #N/A #N/A # /A member 3) UNQ736/ PRO1430

ARHGAP Rho GTPase-activating protein 18 (MacGAP) Q8N392 663 FALSE FALSE FALSE #N/A #N/A #N/A 18 (Rho-type GTPase-activating protein 18)

Rho-associated protein kinase 2 (EC 2.7 .1) (Rho kinase 2) (Rho-associated, coiled-coil- 0 7 KIAA0619 t n P t k s 2 (Rho-associated, 1388 FALSE FALSE FALSE #N/A #N/A #N/A coiled-coii-containing protein kinase II) (ROCK- II) (p164 RGCK-2)

RHOC Rho-related GTP-binding protein RhoC (Rho 193 FALSE FALSE FALSE #N/A #N/A #N/A . _ . ._, cDNA one 9 ) (h9) A K Ribosomal proiein S6 kinase alpha- 1 (S6K- alpha-1) (EC 2.7 11.1) (90 kDa ribosomal RPS6KA1 proiein S6 kinase 1) (p90-RSK 1) (p90RSK1) Q15418 (p90S6K) (MAP kinase-activated protein 735 FALSE TRUE FALSE #N/A #N/A #N/A K1A kinase 1a) (MAPK-aciivated proiein kinase 1a) RSK1 (MAPKAP kinase 1a) (MAPKAPK-1a) (Ribosomal S6 kinase 1) (RSK-1)

Ribosomal protein S6 kinase aipba-3 (S6K- alpha-3) (EC 2.7.1 1.1) (90 kDa ribosomal RPS6KA3 protein S6 kinase 3) (p90-RSK 3) (p90RSK3) ISPK1 (insulin-stimulated protein kinase 1) (iSPK-1) P51812 MAPKAP 740 FALSE TRUE FALSE #N/A #N/A #N/A (MAP kinase-activated protein kinase 1b) K 1B (MAPK-activated protein kinase 1b) (MAPKAP RSK2 kinase 1b) (MAPKAPK-1b) (Ribosomal S6 kinase 2) (RSK-2) (pp90RSK2)

RRP7A Ribosomal RNA-processing protein 7 homoiog Q9Y3A4 280 FALSE FALSE FALSE #N/A #N/A #N/A CG -96 A (Gastric cancer antigen Zg14) SA2 Ribosome biogenesis protein NSA2 bomolog TINP1 095478 (Hairy ce l leukemia protein 1) (TGF-beta- 260 FALSE FALSE FALSE #N/A #N/A #N/A HUSSY- inducible nuclear protein 1) 29 RRS1 Ribosome biogenesis regulatory protein Q15050 KIAA01 12 365 FALSE FALSE FALSE #N/A #N/A #N/A homo!og RRR Ribosome maturation protein SBDS SBDS Q9Y3A5 (Shwachman-Bodian-Diamond syndrome 250 FALSE FALSE FALSE #N/A #N/A #N/A CGI-97 protein) RTCA RNA 3'-terminal phosphate cyclase (RNA cyclase) (RNA-S'-pbosphaie cyclase) (EC 000442 RPC1 6.5.1 .4) (RNA terminal phosphate cyclase 366 FALSE FALSE FALSE #N/A #N/A #N/A RTC1 domain-containing protein 1) (RTC domain- RTCD1 containing protein 1) REX04 RNA exonuciease 4 (EC 3 . .-.-) (Exonuclease Q9GZR2 PMC2 XPMC2) (Prevents mitotic catastrophe 2 422 FALSE TRUE FALSE #N/A #N/A #N/A XPMC2H protein homolog) (hPMC2) Q9H6T3 RPAP3 RNA polymerase -associated protein 3 665 FALSE FALSE FALSE #N/A #N/A #N/A RBM12 RNA-binding protein 12 (RNA-binding motif KIAAQ765 G9NTZ6 protein 12) (SH3/WW domain anchor protein 932 FALSE FALSE FALSE #N/A #N/A #N/A HRIHFB2 in the nucleus) (SWAN) 091

SAM domain-containing protein SAMSN-1 (Hematopoietic adaptor containing SH3 and SAMSN1 Q9NSI8 SAM domains 1) (NasM) (SAM domain, SH3 373 FALSE FALSE FALSE #N/A #N/A #N/A HACS1 domain and nuclear localization signals protein 1) (SH3-SAM adaptor protein)

SEPTS Q92599 Septin-8 483 TRUE FALSE FALSE #N/A #N/A #N/A KIAA0202

Sequestosome-1 (EBI3-associated protein of SQSTM1 60 kDa) (EBIAP) (p60) (Phosphotyrosine- Q13501 ORCA 440 FALSE FALSE FALSE #N/A #N/A #N/A independent ligand for the Lck SH2 domain of OS!L 62 kDa) (Ubiquitin-binding protein p62) Serine protease HTRA2, mitochondrial (EC HTRA2 3 4.21.108) (High temperature requirement 043464 OM protein A2) (HtrA2) (Omi stress-regulated 458 FALSE FALSE FALSE #N/A #N/A #N/A PRSS25 endoprotease) (Serine protease 25) (Serine proteinase OMI) Serine/arginine-rich splicing factor 8 (Pre- SRSF8 mRNA-splicing factor SRP46) (Splicing factor Q9BRL6 SFRS2B 282 FALSE FALSE FALSE #N/A #N/A #N/A SRp46) (Splicing factor, arginine/serine-rich SRP46 2B) ARAF Serine/threonine-protein kinase A-Raf (EC ARAF1 2.7.1 1.1) (Proto-oncogene A-Raf) (Proto- 606 FALSE FALSE FALSE #N/A #N/A #N/A PKS oncogene A-Raf-1) (Proto-oncogene Pks) PKS2 Serine/threonine-protein kinase PLK1 (EC PLK1 PLK 2.7.1 1.21) (Polo-like kinase 1) (PLK-1) 603 FALSE TRUE TRUE #N/A #N/A #N/A (Serine/threonine-protein kinase 13) (STPK13)

Serine/threonine-protein kinase RI01 (EC Q9BRS2 IOK1 568 FALSE FALSE FALSE #N/A #N/A #N/A 2.7.1 1.1) (EC 3.6.3 -) (RIO kinase 1) Serine/threonine-protein phosphatase 4 Q8TF05 EG 1 950 FALSE FALSE FALSE #N/A #N/A #N/A regulatory subunit 1 PP4R1 Serine/threonine-protein phosphatase PP1- gamma catalytic subunit (PP-1G) (EC P36873 PPP1CC 323 TRUE FALSE FALSE #N/A #N/A #N/A 3.1 .3.16) (Protein phosphatase 1C catalytic subunit)

Serine-protein kinase ATM (EC 2.7.1 1.1) Q13315 ATM 3 56 FALSE FALSE FALSE #N/A #N/A #N/A (Ataxia telangiectasia mutated) (A-T mutated)

Serpin B6 (Cytoplasmic antiproteinase) (CAP) (Peptidase inhibitor 6) (PI-6) (Placental 376 FALSE FALSE FALSE #N/A #N/A #N/A thrombin inhibitor)

SERPINB Serpin B9 (Cytoplasmic antiproteinase 3) P50453 376 FALSE FALSE FALSE #N/A #N/A #N/A 9 PI9 (CAP-3) (CAPS) (Peptidase inhibitor 9) (PI-9)

SERPINH Serpin H 1 (47 kDa heat shock protein) 1 CBP1 (Arsenic-transactivated protein 3) (AsTP3) CBP2 P50454 L - (Ce l proliferation-inducing gene 14 protein) 418 FALSE FALSE FALSE #N/A #N/A #N/A (Collagen-binding protein) (Coiiigin) SERPINH (Rheumatoid arthritis-related antigen RA-A47) 2 PIG14 Signal transducer and activator of transcription P52630 STAT2 851 FALSE FALSE FALSE #N/A #N/A #N/A 2 (p1 3) STAT5A Signal transducer and activator of transcription P42229 794 TRUE TRUE TRUE #N/A #N/A #N/A STATS 5A KNSTRN Small kinetochore-associaied protein (SKAP) C15orf23 (Kinetochore-localized astrin-binding protein) SKAP (Kinastrin) (Kinetochore-localized 316 FALSE FALSE FALSE #N/A #N/A #N/A TRAF4AF asirin/SPAGS-binding protein) (TRAF4- 1 HSD1 associated factor 1)

Small proline-rich protein 2D (SPR-2D) (Small P22532 SPRR2D 72 FALSE FALSE FALSE #N/A #N/A #N/A proline-rich protein II) (SPR-H) SU 0 3 Small ubiquitin-related modifier 3 (SUMO-3) S T3A (S T3 homolog 1) (SUMO-2) (Ubiquitin-like 103 FALSE FALSE FALSE #N/A #N/A #N/A S T3H1 protein S T3A) (Smt3A) Solute carrier family 2 , facilitated glucose SLC2A1 transporter member 1 (Glucose transporter P 1 1166 492 FALSE FALSE FALSE #N/A #N/A #N/A GLUT1 type 1, erythrocyte/brain) (GLUT-1) (HepG2 glucose transporter)

SLC35F2 Solute carrier family 35 member F2 374 FALSE FALSE FALSE #N/A #N/A #N/A

SLC43A3 o Solute carrier family 43 member 3 (Protein Q8NBI5 PSEC025 491 FALSE FALSE FALSE #N/A #N/A #N/A FOAP-13)

Sororin (Ceil division cycle-associated protein Q96FF9 CDCA5 252 FALSE TRUE FALSE #N/A #N/A #N/A 5) (p35) Sortiiin ( 0 kDa NT receptor) (Glycoprotein 99523 SORT1 95) (Gp95) (Neurotensin receptor 3) (NTS) 831 FALSE TRUE FALSE #N/A #N/A #N/A (NTR3) )60493 SNX3 Sorting nexin-3 (Protein SDP3) 162 TRUE TRUE FALSE #N/A #N/A #N/A SNX9 Sorting nexin-9 (SH3 and PX domain- SH3PX1 Q9Y5X1 QH3PXD3 'n 9 P te (Protein SDP1) (SH3 and 595 FALSE FALSE FALSE #N/A #N/A #N/A . PX domain-containing protein 3A) A

SPG20 KIAA0610 Spartin (Spastic paraplegia 20 protein) (Trans- Q8N0X7 666 FALSE FALSE FALSE #N/A #N/A #N/A TAHCCP activated by hepatitis C virus core protein 1) 1 SPAST ADPSP Spastin (EC 3.6.4.3) (Spastic paraplegia 4 Q9UBP0 FSP2 616 FALSE FALSE FALSE #N/A #N/A #N/A protein) KIAA1G83 SPG4 SPTA1 Spectrin alpha chain, erythrocytic 1 (Erythroid P02549 2419 FALSE FALSE FALSE #N/A #N/A #N/A SPTA alpha-spectrin) Splicing factor, suppressor of white-apricot SFSWAP homolog (Splicing factor, arginine/serine-rich Q12872 SFRS8 951 FALSE FALSE FALSE #N/A #N/A #N/A 8) (Suppressor of white apricot protein SWAP homolog) CTTN Src substrate cortactin (Amplaxin) (Oncogene Q14247 550 FALSE FALSE FALSE #N/A #N/A #N/A E S 1 EMS1) STE2Q-iike serine/threonine-protein kinase (STE20-iike kinase) (hSLK) (EC 2.7.1 1.1) SLK (CTCL tumor antigen se20-9) (STE20-related Q9H2G2 KIAA02G4 1235 FALSE FALSE FALSE #N/A #N/A #N/A serine/threonine-protein kinase) (STE20- STK2 reiated kinase) (Serine/threonine-protein kinase 2) SDF2L1 Stromal cell-derived factor 2-like protein 1 UNQ1941 Q9HCN8 (SDF2-!ike protein 1) (PWP1 -interacting 221 TRUE TRUE FALSE #N/A #N/A #N/A /PR0442 protein 8)

S A P2 Stromal membrane-associated protein 2 Q8WU79 429 FALSE FALSE FALSE #N/A #N/A #N/A S A P L (Stromal membrane-associated protein 1-like)

Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) P00441 SOD1 154 FALSE FALSE FALSE #N/A #N/A #N/A (Superoxide dismutase 1) (hSodl)

Superoxide dismutase [Mn], mitochondrial (EC 222 FALSE FALSE FALSE #N/A #N/A #N/A 1.15.1.1) SURF6 075683 Surfeit locus protein 6 361 FALSE FALSE FALSE #N/A #N/A #N/A SURF-6 Synaptic functional regulator F R1 (Fragile X Q06787 FMR1 mental retardation protein 1) (F RP) (Protein 632 FALSE FALSE FALSE #N/A #N/A #N/A FMR-1) SYNGR2 043760 UNQ352/ Synaptogyrin-2 (Cellugyrin) 224 FALSE TRUE FALSE #N/A #N/A #N/A PR0615 Synaptosomal-associated protein 23 (SNAP- 000161 SNAP23 23) (Vesicle-membrane fusion protein SNAP- 2 11 FALSE FALSE FALSE #N/A #N/A #N/A 23) Synaptosomal-associated protein 29 (SNAP- 095721 SNAP29 29) (Soluble 29 kDa NSF attachment protein) 258 FALSE FALSE FALSE #N/A #N/A #N/A (Vesicle-membrane fusion protein SNAP-29)

Q86Y82 STX12 Syntaxin-12 276 FALSE FALSE FALSE #N/A #N/A #N/A STX5 Q13190 Syntaxin-5 3 F S ! F S FA L #N/A #N/A #N/A STX5A 015400 STX7 Syntaxin-7 261 FALSE FALSE FALSE #N/A #N/A #N/A Telomere-associated protein RIF1 (Rap1- Q5UIP0 RIF1 2472 F ! FALSEi FALSE #N/A #N/A #N/A interacting factor 1 homolog) TE 3 Teneurin-3 (Ten-3) (Protein Odd Oz/ten-m KIAA1455 Q9P273 homolog 3) (Tenascin-M3) (Ten-m3) 2699 FALSE FA L E #N/A #N/A #N/A ODZ3 (Teneurin transmembrane protein 3) TN 3 Q9UGI8 TES Tesfin (TESS) 421 FALSE FALSE FALSE #N/A #N/A #N/A Tetratricopeptide repeat protein 27 (TPR Q6P3X3 TTC27 843 FALSE FALSE FALSE #N/A #N/A #N/A repeat protein 27)

TF!IH basal transcription factor complex helicase XPD subunit (EC 3.6.4.12) (Basic transcription factor 2 80 kDa subunit) (BTF2 ERCC2 p80) (CXPD) (DNA excision repair protein P18074 XPD ERCC-2) (DNA repair protein complementing 760 FALSE FALSE FALSE #N/A #N/A #N/A XPDC XP-D ceils) (TFIIH basal transcription factor complex 80 kDa subunit) (TFIIH 80 kDa subunit) (TFIIH p80) (Xeroderma pigmentosum group D-complementing protein)

Thiopurine S-methyltransferase (EC 2.1 . 1 .67) P51580 TP T 245 FALSE FALSE FALSE #N/A #N/A #N/A (Thiopurine methyitransferase) Thioredoxin domain-containing protein 9 (ATP- TXNDC9 014530 binding protein associated with eel! 226 FALSE FALSE FALSE #N/A #N/A #N/A APACD differentiation) (Protein 1-4) TXNRD2 Thioredoxin reductase 2 , mitochondria! (EC Q9NNW7 KIAA16S2 1.8.1 .9) (Selenoprotein Z) (Se!Z) (TR-beta) 524 FALSE FALSE FALSE #N/A #N/A #N/A TRXR2 (Thioredoxin reductase TR3) THUMPD THUMP domain-containing protein 3 5 7 TRUE FALSE FALSE #N/A #N/A #N/A 3 P04183 TK1 Thymidine kinase, cytosoiic (EC 2.7.1 .21) 234 FALSE FALSE FALSE #N/A #N/A #N/A THADA Thyroid adenoma-associated protein (Gene Q6YHU6 G TA 1953 FALSE FALSE FALSE #N/A #N/A #N/A inducing thyroid adenomas protein) KIAA1767 Thyroid receptor-interacting protein 6 (TR- TRIP6 interacting protein 6) (TRIP-6) (Opa- Q15654 476 FALSE FALSE FALSE #N/A #N/A #N/A OIP1 interacting protein 1) (OIP-1) (Zyxin-re!ated protein 1) (ZRP-1)

TOR1A1P Torsin-1A-interacting protein 2 (Lumenal Q8NFQ8 2 IFRG15 470 FALSE FALSE FALSE #N/A #N/A #N/A domain-like LAP1) LULL1

TRAFD1 TRAF-type zinc finger domain-containing 0 14545 582 FALSE FALSE FALSE #N/A #N/A #N/A FLN29 protein 1 (Protein FLN29) Transient receptor potential cation channel TRPV2 subfamily V member 2 (TrpV2) (Osm-9-iike Q9Y5S1 764 FALSE FALSE FALSE #N/A #N/A #N/A VRL TRP channel 2) (OTRPC2) (Vanilloid receptor like protein 1) (VRL-1) Translation initiation factor elF-2B subunit EIF2B1 Q14232 alpha (elF-2B GDP-GTP exchange factor 305 FALSE FALSE FALSE #N/A #N/A #N/A EIF2BA subunit alpha) Translation initiation factor elF-2B subunit EIF2B5 Q13144 epsilon (e!F-2B GDP-GTP exchange factor 721 FALSE FALSE FALSE #N/A #N/A #N/A EIF2BE subunit epsilon) Translation initiation factor IF-2, mitochondrial MTIF2 727 FALSE FALSE FALSE #N/A #N/A #N/A (IF-2(Mt)) (IF-2Mt) (IF2(mt)) Transmembrane channel-like protein 1 Q8TDI8 T C1 (Transmembrane cochlear-expressed protein 760 FALSE FALSE FALSE #N/A #N/A #N/A 1) Transmembrane emp24 domain-containing T ED2 Q15363 proiein 2 (Membrane protein p24A) (p24) (p24 201 FALSE FALSE FALSE #N/A #N/A #N/A RNP24 family protein beta-1) (p24beta1) T ED5 Transmembrane emp24 domain-containing CGI-100 Q9Y3A6 protein 5 (p24 family protein gamma-2) 229 FALSE FALSE FALSE #N/A #N/A #N/A UNQ397/ (p24gamma2) (p28) PR0733 TMEM131 Q92545 KIAA0257 Transmembrane protein 131 (Protein RW1) 1883 FALSE FALSE FALSE #N/A #N/A #N/A RW1

T E 192 Transmembrane protein 192 271 FALSE FALSE FALSE #N/A #N/A #N/A TMEM214 oe Q6NUQ4 Transmembrane protein 214 689 TRUE FALSE FALSE #N/A #N/A #N/A PP446 tRNA (guanine(26)-N(2))-dimethyltransferase (EC 2.1 . 1 .216) (tRNA 2,2-dimethyiguanosine- Q9NXH9 TRMT1 26 methyltransferase) (tRNA(guanine-26,N(2)- 659 TRUE FALSE FALSE #N/A #N/A #N/A N(2)) methyltransferase) (tRNA(m(2,2)G26)dimethyltransferase)

tRNA (guanine-N(7)-)-methyltransferase non- P57081 WDR4 catalytic subunit WDR4 (WD repeat- 412 TRUE FALSE FALSE #N/A #N/A #N/A containing protein 4) RMT2A ( ^~5-)-methyltransferase homolog A Q8IZ69 (EC 2.1 . 1 .-) (Hpa tiny fragments locus 9c 625 TRUE FALSE FALSE #N/A #N/A #N/A HTF9C protein) TSEN15 tRNA-splicing endonuciease subunit Sen15 Q8WW01 C1orf19 (SEN15 homolog) (HsSEN15) (tRNA-intron 171 FALSE FALSE FALSE #N/A #N/A #N/A SEN15 endonuciease Sen1 5) tRNA-splicing endonuclease subunit Sen34 TSEN34 (EC 4.6.1 16) (Leukocyte receptor cluster Q9BSV6 LENG5 310 FALSE FALSE FALSE #N/A #N/A #N/A member 5) (tRNA-intron endonuclease Sen34) SEN34 (HsSen34) TUBB2A Q13885 Tubulin beta-2A chain (Tubulin beta class lla) 445 FALSE FALSE FALSE #N/A #N/A #N/A TUBB2 Type 2 phosphatidylinositol 4,5-bisphosphate T E 55 4-phosphatase (Type 2 Ptdlns-4,5-P2 4- Q8N4L2 257 FALSE FALSE FALSE #N/A #N/A #N/A A Ptase) (EC 3.1 .3.78) (Ptdins-4,5-P2 4-Ptase ) (Transmembrane protein 55A)

AGTRAP Type-1 angiotensin II receptor-associated Q6RW13 159 FALSE FALSE FALSE #N/A #N/A #N/A ATRAP protein (AT1 receptor-associated protein) Tyrosine-protein kinase BTK (EC 2.7.10.2) BTK (Agammaglobulinemia tyrosine kinase) (ATK) Q06187 AG 1 659 FALSE FALSE FALSE #N/A #N/A #N/A (B-ceil progenitor kinase) (BPK) (Bruton ATK BPK tyrosine kinase)

Tyrosine-protein kinase Lyn (EC 2.7.10.2) (Lck/Yes-related novel protein tyrosine kinase) P07948 LYN J Ko ...... , . , , . , 512 FALSE FALSE FALSE #N/A #N/A # /A (V-yes-1 Yamaguchj sarcoma viral related oncogene homolog) (p53Lyn) (p56Lyn)

YES1 Tyrosine-protein kinase Yes (EC 2.7.10.2) P07947 543 FALSE FALSE FALSE #N/A #N/A #N/A YES (Proto-oncogene c-Yes) (p61-Yes) Tyrosine-protein phosphatase non-receptor Q05209 PTPN12 type 12 (EC 3.1.3.48) (PTP-PEST) (Protein- 780 FALSE FALSE FALSE #N/A #N/A #N/A tyrosine phosphatase G1) (PTPG1) Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) (His domain-containing PTPN23 Q9H3S7 protein tyrosine phosphatase) (HD-PTP) 1636 FALSE FALSE FALSE #N/A #N/A #N/A KIAA1471 (Protein tyrosine phosphatase TD14) (PTP- TD14) YARS2 Tyrosine-tRNA iigase, mitochondrial (EC Q9Y2Z4 477 FALSE FALSE FALSE #N/A #N/A #N/A CG -04 6.1 . 1 .1) (Tyrosyl-tRNA synthetase) (TyrRS) UTP14A U3 small nucleolar RNA-associated proiein 14 Q9BVJ6 SDCCAG homolog A (Antigen NY-CO-16) (Serologically 771 FALSE FALSE FALSE #N/A #N/A #N/A 16 defined colon cancer antigen 16)

UBQLN4 Ubiquilin-4 (Ataxin-1 interacting ubiquitin-like C1orf6 protein) (A1 Up) (Ataxin-1 ubiquitin-like- Q9NRR5 601 FALSE FALSE FALSE #N/A #N/A #N/A CIP75 interacting protein A 1U) (Connexin43- UBiN interacting protein of 75 kDa) (CIP75)

Ubiquitin carboxyl-terminal hydrolase 15 (EC USP15 3.4.19.12) (Deubiquitinating enzyme 15) Q9Y4E8 981 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0529 (Ubiquitin thioesterase 15) (Ubiquitin-specific- processing protease 15) (Unph-2) (Unph4)

Ubiquitin carboxyl-terminal hydrolase 16 (EC 3.4.19.12) (Deubiquitinating enzyme 16) USP16 Q9Y5T5 (Ubiquitin thioesterase 16) (Ubiquitin- 823 FALSE FALSE FALSE #N/A #N/A #N/A /ISTP039 processing protease UBP-M) (Ubiquitin- specific-processing protease 16) oe Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.4.19.12) (Deubiquitinating enzyme 3) Q9Y6I4 USPS 520 FALSE FALSE FALSE #N/A #N/A #N/A (Ubiquitin thioesterase 3) (Ubiquitin-specific- processing protease 3) Ubiquitin carboxyl-terminal hydrolase 48 (EC 3.4.19.12) (Deubiquitinating enzyme 48) Q86UV5 (Ubiquitin thioesterase 48) (Ubiquitin-specific 1035 FALSE FALSE FALSE #N/A #N/A #N/A USP31 peptidase 48) (Ubiquitin-specific protease 48) (Ubiquitin-specific-processing protease 48)

YOD1 DUBA8 Ubiquitin thioesterase OTU1 (EC 3.4.19.12) Q5VVQ6 HIN7 (DUBA-8) (H -1-induced protease 7) (HIN-7) 348 FALSE FALSE FALSE #N/A #N/A #N/A OTUD2 (HsHIN7) (OTU domain-containing protein 2) PRO0907 Ubiquitin thioesierase OTUB1 (EC 3.4.19.12)

Q (Deubiquitinating enzyme OTUB1) (OTU Q96FW1 O U domain-containing ubiquitin aldehyde-binding 271 FALSE FALSE FALSE #N/A #N/A #N/A HSPC263 p ) ( ' ) (hOTU1) (Ubiquitin- specific-processing protease OTUB1) Ubiquitin-associated domain-containing UBAC1 protein 1 (UBA domain-containing protein 1) GBDR1 (E3 ubiquitin-protein ligase subunit KPC2) Q9BSL1 4 5 TRUE FALSE FALSE #N/A #N/A #N/A KPC2 (Giialb!astoma cell differentiation-related UBADC1 protein 1) (Kip1 ubiquitination-promoting complex protein 2) Ubiquitin-conjugating enzyme E2 D3 (EC 2.3.2.23) ((E3-independent) E2 ubiquitin- UBE2D3 conjugating zyme D3) (EC 2.3.2.24) (E2 g Q-.. UBC5C -co jugating enzyme D3) (Ubiquitin 147 FALSE FALSE FALSE #N/A #N/A #N/A UBCH5C r P o te ' 3) (Ubiquitin-conjugating w enzyme E2(17)KB 3) (Ubiquitin-conjugating enzyme E2-17 kDa 3) (Ubiquitin-protein ligase D3) Ubiquitin-conjugating enzyme E2 K (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme K) (Huntingtin-interacting protein 2) (HIP-2) UBE2K (Ubiquitin carrier protein) (Ubiquitin- P61086 2 0 TRUE TRUE FALSE #N/A #N/A #N/A HIP2 L G conjugating enzyme E2-25 kDa) (Ubiquitin- conjugating enzyme E2(25K)) (Ubiquitin- conjugating enzyme E2-25K) (Ubiquitin- protein ligase)

UDP-N-acetyihexosamine pyrophosphorylase (Antigen X) (AGX) (Sperm-associated antigen UAP1 2) [Includes: UDP-N-acetyigalactosamine Q16222 522 FALSE FALSE FALSE #N/A #N/A #N/A SPAG2 pyrophosphorylase (EC 2.7.7.83) (AGX-1); UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) (AGX-2)] Q5VZ46 KIAA1614 Uncharacterized protein KIAA1614 1190 FALSE FALSE FALSE #N/A #N/A #N/A Unconventional rnyosin-lc (Myosin i beta) 000159 1Y01C 1063 FALSE FALSE FALSE #N/A #N/A #N/A (MM!-beta) (MMIb) Uroporphyrinogen decarboxylase (UPD) (URO- P06132 UROD 367 FALSE FALSE FALSE #N/A #N/A #N/A D) (EC 4.1 1 .37) Uroporphyrinogen-!!! synthase (UROI!IS) (UROS) (EC 4.2.1.75) (Hydroxymethylbilane P10746 UROS 265 FALSE FALSE FALSE #N/A #N/A #N/A hydroiyase [cyclizing]) (Uroporphyrinogen-!!! cosynthase)

UTP-glucose-1 -phosphate uridyly!transferase UGP2 Q16851 (EC 2.7.7.9) (UDP-g!ucose 508 FALSE FALSE FALSE #N/A #N/A #N/A UGP1 pyrophosphorylase) (UDPGP) (UGPase)

V P1 TDC1 Vacuole membrane protein 1 Q96GC9 406 FALSE FALSE FALSE #N/A #N/A #N/A TME 49 (Transmembrane protein 49) HSPC292 Vesicle-associated membrane protein 7 VAMP7 P51809 (VAMP-7) (Synaptobrevin-!ike protein 1) 220 TRUE FALSE FALSE #N/A #N/A #N/A SYBL1 (Tetanus-insensitive VAMP) (Ti-VAMP) Vesicle-associated membrane protein 8 Q9BV40 VAMPS 100 FALSE FALSE FALSE #N/A #N/A #N/A (VAMP-8) (Endobrevin) (EDB) P18206 VCL Vinculin (Metavinculin) (MV) 1134 FALSE FALSE FALSE #N/A #N/A #N/A Vitronectin (VN) (S-protein) (Serum-spreadinc factor) (V75) [Cleaved into: Vitronectin V65 P04004 VTN 478 FALSE FALSE FALSE #N/A #N/A #N/A subunit; Vitronectin V10 subunit; Somatomedin-Bl V-type proton ATPase 6 kDa subunit a isoform 1 (V~ATPase 116 kDa isoform a1) ATP6V0A (Clathrin-coated veside/synaptic vesicle 1 ATP6N1 proton pump 116 kDa subunit) (Vacuolar Q93050 837 FALSE TRUE FALSE #N/A #N/A #N/A ATP6N1A adenosine triphosphatase subunit Ac1 16) VPP1 (Vacuolar proton pump subunit 1) (Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1) V-type proton ATPase 116 kDa subunit a isoform 2 (V-ATPase 116 kDa isoform a2) ATP6V0A (Lysosomal H(-^-transporting ATPase V O Q9Y487 856 FALSE FALSE FALSE #N/A #N/A #N/A 2 subunit a2) (TJ6) (Vacuolar proton translocating ATPase 116 kDa subunit a isoform 2) V-type proton ATPase subunit d 1 (V-ATPase ATP6V0D subunit d 1) (32 kDa accessory protein) (V- P61421 1 ATP6D ATPase 4 kDa accessory protein) (V-ATPase 351 FALSE TRUE FALSE #N/A #N/A #N/A w VPATPD AC39 subunit) (p39) (Vacuolar proton pump subunit d 1)

ATP6V1E V-type proton ATPase subunit E 1 (V-ATPase P36543 1 ATP6E subunit E 1) (V-ATPase 3 1 kDa subunit) (p31) 226 F . FALSE F . #N/A #N/A #N/A ATP6E2 (Vacuolar proton pump subunit E 1)

Q9BV38 WDR18 W D repeat-containing protein 18 432 FALSE TRUE TRUE #N/A #N/A #N/A Q9NNW5 WDR6 W D repeat-containing protein 6 1121 FALSE FALSE FALSE #N/A #N/A #N/A WDR74 W D repeat-containing protein 74 (NOP seven- Q6RFH5 385 FALSE FALSE FALSE #N/A #N/A #N/A NSA1 associated protein 1) Q9H967 WDR76 W D repeat-containing protein 76 626 FALSE FALSE FALSE #N/A #N/A #N/A WRN r syndrome ATP-dependent helicase (EC 3.6 .4 .12) (DNA helicase, RecQ-like type 1432 FALSE FALSE FALSE #N/A #N/A #N/A RECQL2 ( R Q ) (E s ) (E 3.1 .-.-) (RecQ protein-like 2) Xenotropic and polytropic retrovirus receptor 1 XPR1 (Protein SYG1 homolog) (Xenotropic and Q9UBH6 696 FALSE FALSE FALSE #N/A #N/A #N/A SYG1 X R polytropic murine leukemia virus receptor X3) (X-receptor) YrdC domain-containing protein, mitochondrial YRDC (Dopamine receptor-interacting protein 3) Q86U90 DRIPS 279 FALSE TRUE FALSE #N/A #N/A #N/A (Ischemia/reperfusion-inducible protein IRIP homo!og) (hIRIP) YTHDC1 YTH domain-containing protein 1 (Splicing Q96 U7 KIAA1966 727 FALSE FALSE FALSE #N/A #N/A #N/A factor YT521) (YT521-B) YT521 Zinc finger and BTB domain-containing protein 095625 ZBTB1 1053 FALSE FALSE FALSE #N/A #N/A #N/A 11

ZFC3H1 Zinc finger C3H1 domain-containing protein CCDC131 060293 (Coiled-coil domain-containing protein 131) 1989 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0546 (Proline/serine-rich coiled-coii protein 2) PSRC2

Q9UL36 ZNF236 Zinc finger protein 236 1845 FALSE FALSE FALSE #N/A #N/A #N/A ZNF622 Zinc finger protein 622 (Zinc finger-like protein Q969S3 477 FALSE FALSE FALSE #N/A #N/A #N/A o ZPR9 9)

3 ∆ ZNT5 Zinc transporter 5 (ZnT-5) (Solute carrier ZNTL1 Q8TAD4 family 30 member 5) (ZnT-like transporter 1) 765 FALSE FALSE FALSE #N/A #N/A # /A ZTL1 (hZTL1) UNQ863/ PR01879

SLC39A1 Zinc transporter ZIP14 (LIV-1 subfamily of Z P 4 zinc transporter 4) (LZT-Hs4) (Solute carrier Q15043 492 FALSE FALSE FALSE #N/A #N/A #N/A KIAA0062 family 39 member 14) (Zrt- and Irt-like protein ZIP14 14) (ZIP-14)

SLC2A14 Solute carrier family 2 , facilitated glucose Q8TDB8 GLUT14 transporter member 14 (Glucose transporter 520 FALSE FALSE FALSE #N/A #N/A #N/A GLUT3 type 14) (GLUT- 14) RB 27 RNA-binding protein 27 (RNA-binding motif Q9P2N5 1060 FALSE FALSE FALSE #N/A #N/A #N/A KIAA131 1 protein 27)

Cyciin-dependent kinase 1B (EC 2 7. 1.22) CDK1 1B (Cell division cycle 2-like protein kinase 1) CDC2L1 (CLK-1) (Cell division protein kinase 1 B) P21 127 CDK1 795 TRUE FALSE FALSE #N/A #N/A #N/A (Gaiactosyltransferase-associated protein PITSLRE kinase p58/GTA) (PITSLRE serine/threonine- A PK58 protein kinase CDC2L1) (p58 CLK-1)

Fumarylacetoacetate hydrolase domain- Q6P213 FAHD2B 314 FALSE FALSE FALSE #N/A #N/A #N/A containing protein 2B (EC 3.-.-.-)

Eukaryotic translation initiation factor 1A, Y- 014602 EIF1AY chromosomal (elF-1A Y isoform) (Eukaryotic 144 FALSE FALSE FALSE #N/A #N/A #N/A translation initiation factor 4C) (elF-4C)

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1 .149) (1- phosphatidylinositoi 5-phosphate 4-kinase 2- P ! beta) (Diphosphoinositide kinase 2-beta) P78356 416 FALSE FALSE FALSE #N/A #N/A #N/A PIP5K2B (Phosphatidylinositol 5~phosphate 4-kinase type II beta) (PI(5)P 4-kinase type I beta) (PIP4KN-befa) (Ptdlns(5)P-4-kinase isoform 2- beta) PRKACA cAMP-dependent protein kinase catalytic P17612 351 FALSE FALSE FALSE #N/A #N/A #N/A PKACA subunit alpha (PKA C-alpha) (EC 2.7.1 . 1 1)

Interferon-induced transmembrane protein 3 QQ1628 F T 3 (Dispanin subfamily A member 2b) (DSPA2b) 133 TRUE TRUE TRUE #N/A #N/A #N/A (Interferon-inducible protein 1-8U) Choline-phosphaie cytidylyltransferase B (EC PCYT1 B 2.7.7.15) (CCT-beta) (CTRphosphocholine Q9Y5K3 36 FALSE FALSE FALSE #N/A #N/A #N/A CCTB cytidylyltransferase B) (CCT B) (CT B) (Phosphory!choline transferase B)

Guanine nucleotide-binding protein subunit GNA1 1 alpha-1 (G alpha-1 1) (G-protein subunit P29992 FALSE FALSE FALSE #N/A #N/A #N/A GA.11 alpha- ) (Guanine nucieotide-binding protein G(y) subunit alpha) G antigen 1 (GAGE-1) (Antigen Z2-F) Q 13065 GAGE1 13S FALSE FALSE FALSE #N/A #N/A #N/A (Cancer/testis antigen 4.1) (CT4.1) umrnary of a e s equency < tiffed PSMs (at FDR 1%) n tryptic digests J exposed indicated compound (50

Grand with at photo- ce!ecoxib Protein name Tota least one n anaiog 9 (PS s) photo-

10 kDa heat shock protein, mitochondrial OS=Homo FALSE sapiens GN=HSPE1 PE=1 SV 2 116 kDa U5 small nuclear ribonucleoprotein component OS=Homo sapiens GN=EFTUD2 PE=1 FALSE SV=1 14-3-3 protein beta/alpha OS^Homo sapiens FALSE GN=YWHAB PE=1 SV=3 1 4 14-3-3 protein epsilon OS=Homo sapiens FALSE GN=YWHAE PE=1 SV=1 1 1 14-3-3 protein gamma OS=Homo sapiens TRUE GN=YWHAG PE=1 SV=2 14-3-3 protein iheta OS=Homo sapiens TRUE GN=YWHAQ PE=1 SV=1 1 2 14-3-3 protein zeta/delta OS=Homo sapiens FALSE GN=YWHAZ PE=1 SV=1 2 2 2-oxoglutarate dehydrogenase, mitochondrial TRUE OS=Homo sapiens GN=OGDH PE=1 SV=3 26S protease regulatory subunit 6A OS=Homo TRUE sapiens GN=PSMC3 PE=1 SV=3 26S protease regulatory subunit 6B QS=Homo TRUE sapiens GN=PSMC4 PE=1 SV=2 26S protease regulatory subunit 8 OS=Homo FALSE sapiens GN=PSMC5 PE=1 SV=1 1 26S proteasome non-ATPase reguiatory subunit 2 FALSE OS=Homo sapiens GN=PSMD2 PE=1 SV=3 3 3-hydroxyacyi-CoA dehydrogenase type-2 TRUE OS^Homo sapiens GN=HSD17B10 PE=1 SV=3 40S ribosomal protein S10 OS=Homo sapiens FALSE GN=RPS10 PE=1 SV=1 1 1 4QS ribosomal protein S12 OS=Horno sapiens FALSE GN=RPS12 PE=1 SV=3 1 2 4QS ribosomal protein S13 OS=Homo sapiens TRUE GN=RPS13 PE=1 SV=2 1 4QS ribosomal protein S14 OS=Homo sapiens TRUE GN=RPS14 PE=1 SV=3 4QS ribosomal protein S15 OS=Homo sapiens TRUE GN=RPS15 PE=1 SV=2 1 40S ribosomal protein S15a OS=Homo sapiens TRUE GN=RPS15A PE=1 SV=2 4 40S ribosomal protein S16 OS=Homo sapiens TRUE GN=RPS16 PE=1 SV=2 1 40S ribosomal protein S17 OS=Homo sapiens FALSE GN=RPS17 PE=1 SV=2 3 40S ribosomal protein S20 OS=Homo sapiens FALSE GN=RPS20 PE=1 SV=1 1 40S ribosomal protein S27 OS=Homo sapiens FALSE GN=RPS27 PE=1 SV=3 1 40S ribosomal protein S3 OS=Homo sapiens TRUE GN=RPS3 PE=1 SV=2 5 40S ribosomal protein S3a OS=Homo sapiens TRUE GN=RPS3A PE=1 SV=2 1 40S ribosomal protein S4, X isoform OS=Homo FALSE sapiens GN=RPS4X PE=1 SV=2 40S ribosomal protein S5 OS=Homo sapiens FALSE GN=RPS5 PE=1 SV=4 40S ribosomal protein S7 OS=Homo sapiens TRUE GN=RPS7 PE=1 SV=1 40S ribosomal protein S8 OS=Homo sapiens FALSE GN=RPS8 PE=1 SV=2 1 1 40S ribosomal protein SA OS=Homo sapiens FALSE GN=RPSA PE=1 SV=4 4F2 cell-surface antigen heavy chain OS=Homo TRUE sapiens GN=SLC3A2 PE=1 SV=3 6 S'-AMP-activated protein kinase subunit garnma~1 TRUE OS=Homo sapiens GN=PRKAG1 PE=1 SV=1 1 6 kDa heat shock protein, mitochondria! OS=Homo sapiens GN=HSPD1 PE=1 SV=2 26 14 9 1 60S acidic ribosomal protein P O OS=Homo sapiens - FALSE GN=RPLP0 PE=1 SV=1 1 2 60S acidic ribosomal protein P 1 OS=Homo sapiens GN=RPLP1 PE=1 SV=1 1 1 4 S 60S ribosomal protein L 2 OS=Homo sapiens GN=RPL12 PE=1 SV=1 2 4 9 L S 60S ribosomal protein L 3 GS=Homo sapiens FALSE GN=RPL13 PE=1 SV=4 1 1 60S ribosomal protein L 4 OS=Homo sapiens FALSE GN=RPL14 PE=1 SV 4 1 1 60S ribosomal protein L OS=Homo sapiens TRUE GN=RPL17 PE=1 SV=3 60S ribosomal protein L 8 OS=Homo sapiens FALSE GN=RPL18 PE=1 SV=2 1 1 60S ribosomal protein L18a OS=Homo sapiens GN=RPL18A PE=1 SV=2 1 2 T R 60S ribosomai protein L 9 OS=Homo sapiens „ FALSE GN=RPL19 PE=1 SV=1 1 1 60S ribosomai protein L21 OS=Homo sapiens . TRUE GN=RPL21 PE=1 SV=2 2. 60S ribosomai protein L22 OS=Homo sapiens FALSE GN=RPL22 PE=1 SV=2 1 60S ribosomai protein L23 OS=Homo sapiens TRUE GN=RPL23 PE=1 SV=1 60S ribosomai protein L24 OS=Homo sapiens TRUE GN=RPL24 PE=1 SV=1 1 60S ribosomai protein L27 OS=Homo sapiens GN=RPL27 PE=1 SV=2 1 2 60S ribosomai protein L27a OS=Homo sapiens FALSE GN=RPL27A PE=1 SV=2 1 Z 60S ribosomai protein L3 GS=Homo sapiens FALSE GN=RPL3 PE=1 SV=2 1 1 60S ribosomal protein L30 OS=Homo sapiens TRUE GN=RPL30 PE=1 SV=2 2 60S ribosomal protein L36a OS=Homo sapiens FALSE GN=RPL36A PE=1 SV=2 1 60S ribosomal protein L38 OS=Homo sapiens TRUE GN=RPL38 PE=1 SV 2 2 60S ribosomal protein L4 0 =Homo sapiens TRUE GN=RPL4 PE=1 SV=5 60S ribosomal protein L7 OS=Homo sapiens FALSE GN=RPL7 PE=1 SV=1 60S ribosomal protein L7a GS=Homo sapiens TRUE GN=RPL7A PE=1 SV=2 60S ribosomal protein L8 OS=Homo sapiens FALSE GN=RPL8 PE=1 SV=2 1 1 60S ribosomal protein L9 OS=Homo sapiens TRUE GN=RPL9 PE=1 SV=1 1 1 78 kDa glucose-regulated protein OS=Homo FALSE sapiens GN=HSPA5 PE=1 SV=2 3 11 9 26 A-kinase anchor protein 1, mitochondrial OS=Homo FALSE sapiens GN=AKAP1 PE=1 SV=1 1 1 Acetyl-CoA acetyltransferase, mitochondrial FALSE OS=Homo sapiens GN=ACAT1 PE=1 SV=1 1 1 Acidic ieucine-rich nuclear phosphoprotein 32 family member A OS=Homo sapiens GN=ANP32A PE=1 TRUE SV=1 1 Actin-related protein 2/3 complex subunit 3 TRUE OS=Homo sapiens GN=ARPC3 PE=1 SV=3 1 2 Actin-related protein 3 OS=Homo sapiens TRUE GN=ACTR3 PE=1 SV=3 1 2 Actin, alpha skeletal muscle GS=Homo sapiens TRUE GN=ACTA1 PE=1 SV=1 1 1 2 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB F A ! PE=1 SV=1 7 6 3 29 Adenine phosphoribosyltransferase OS=Homo FALSE sapiens GN=APRT PE=1 SV=2 1 1 Adenosine deaminase OS=Homo sapiens GN=ADA FALSE PE=1 SV=3 1 2 4 Adenosylhomocysteinase OS=Homo sapiens FALSE GN=AHCY PE=1 SV=4 1 2 2 7 Adenylate kinase 2 , mitochondrial OS=Homo FALSE sapiens GN=AK2 PE=1 SV=2 1 1 Adenylosuccinate lyase OS=Homo sapiens - TRUE GN=ADSL PE=1 SV=2 Adenyiyl cyclase-associated protein 1 OS^Homo FALSE sapiens GN=CAP1 PE=1 SV=5 ADP-ribosy!ation factor 3 OS=Homo sapiens TRUE GN=ARF3 PE=1 SV=2 1 ADP-ribosylation factor-like protein 1 OS=Homo TRUE sapiens GN=ARL1 PE=1 SV=1 1 ADP/ATP transiocase 2 OS=Homo sapiens TRUE GN=SLC25A5 PE=1 SV=7 1 ADP/ATP transiocase 3 OS=Homo sapiens FALSE GN=SLC25A6 PE=1 SV=4 1 1 1 3

Aladin GS=Homo sapiens GN=AAAS PE=1 SV=1 -j TRUE Alanine-tRNA ligase, cytoplasmic OS=Homo TRUE sapiens GN=AARS PE=1 SV=2 1 3 Aldose reductase OS=Homo sapiens GN=AKR1 B 1 TRUE PE=1 SV=3 1 Alpha-actinin-1 OS=Homo sapiens GN=ACTN1 TRUE PE=1 SV=2 1 4 Alpha-enoiase OS=Homo sapiens GN=EN01 PE=1 FALSE SV 2 4 1 9 Annexin A 1 OS=Homo sapiens GN=ANXA1 PE-1 SV=2 TRUE Antigen Ki-67 OS=Homo sapiens GN KI67 PE=1 TRUE SV=2 1 APC membrane recruitment protein 3 OS=Homo FALSE sapiens GN=AMER3 PE=1 SV=2 1 ATP synthase F(0) complex subunit B 1, mitochondrial OS=Homo sapiens GN=ATP5F1 TRUE PE=1 SV=2 ATP synthase subunit alpha, mitochondrial FALSE OS=Homo sapiens GN=ATP5A1 PE=1 SV=1 5 5 2 20 ATP synthase subunit beta, mitochondrial FALSE OS=Homo sapiens GN=ATP5B PE=1 SV=3 8 10 2 3 1 ATP synthase subunit f , mitochondrial OS=Homo TRUE sapiens GN=ATP5J2 PE=1 SV=3 1 1 ATP synthase subunit gamma, mitochondrial TRUE OS=Homo sapiens GN=ATP5C1 PE=1 SV=1 ATP-binding cassette sub-family D member 3 TRUE OS=Homo sapiens GN=ABCD3 PE=1 SV=1 2 2 ATP-binding cassette sub-family E member 1 TRUE S H mo sapiens GN=ABCE1 PE=1 SV=1 1 1 ATP-citrate synthase OS=Homo sapiens GN=ACLY TRUE PE=1 SV=3 1 2 ATP-dependent 6-phosphofructokinase, platelet type TRUE OS=Homo sapiens GN=PFKP PE=1 SV=2 1 1 ATP-dependent RNA heiicase A OS=Homo sapiens FALSE GN=DHX9 PE=1 SV 4 4 3 4 16 ATP-dependent RNA heiicase DDX1 OS=Homo TRUE sapiens GN=DDX1 PE=1 SV=2 1 2 ATP-dependent RNA heiicase DDX18 OS=Homo TRUE sapiens GN=DDX18 PE=1 SV=2 1 2 ATP-dependent RNA heiicase DDX39A OS=Homo TRUE sapiens GN=DDX39A PE=1 SV=2 4 1 8 ATP-dependent RNA heiicase DDX3X OS=Homo FALSE sapiens GN=DDX3X PE=1 SV=3 6 3 1 15 ATP-dependent RNA heiicase DDX50 OS=Homo TRUE sapiens GN=DDX50 PE=1 SV=1 B-ceil lymphoma/leukemia 1 B OS=Homo sapiens TRUE GN=BCL1 B PE=1 SV=1 Beta-enolase OS=Homo sapiens GN=EN03 PE=1 FALSE SV=5 1 1 3 5 Bifunctional epoxide hydrolase 2 OS^Homo sapiens FALSE GN=EPHX2 PE=1 SV=2 Bifunctional purine biosynthesis protein PURH TRUE OS=Homo sapiens GN=AT!C PE=1 SV=3 1 1 3 Calreticulin OS=Homo sapiens GN=CALR PE=1 TRUE SV=1 cAMP-dependent protein kinase type l-alpha regulatory subunit OS=Homo sapiens TRUE GN=PRKAR1A PE=1 SV=1 1 1 Cancer-related nucleoside-triphosphatase FALSE OS=Homo sapiens GN=NTPCR PE=1 SV=1 1 1 Cathepsin D OS=Homo sapiens GN=CTSD PE=1 TRUE SV=1 2 2 5 Cell cycle and apoptosis regulator protein 2 FALSE OS=Homo sapiens GN=CCAR2 PE=1 SV=2 1 1 Centromere protein T OS=Homo sapiens TRUE GN=CENPT PE=1 SV=2 1 Centrosome-associated protein 350 OS=Homo TRUE sapiens GN=CEP350 PE=1 SV=1 1 1 2 Charged multivesicular body protein 7 OS=Homo TRUE sapiens GN=CHMP7 PE=1 SV=1 1 1 Chloride intracellular channel protein 1 OS=Homo FALSE sapiens GN=CLIC1 PE=1 SV=4 2 2 Clathrin heavy chain 1 OS=Homo sapiens FALSE GN=CLTC PE=1 SV=5 3 3 1 10 Cleavage and polyadenylation specificity factor subunit 5 OS=Homo sapiens GN=NUDT21 PE=1 TRUE SV=1 1 1 3 Cleavage and polyadenylation specificity factor subunit 6 OS=Homo sapiens GN=CPSF6 PE=1 FALSE SV=2 Cleavage and polyadenylation specificity factor TRUE

FALSE Complement component 1 Q subcomponent-binding protein, mitochondrial OS=Homo sapiens FALSE GN=C1QBP PE=1 SV=1 1 1 Copine-1 OS=Horno sapiens GN=CPNE1 PE=1 TRUE SV=1 2 4 Core histone macro-H2A 1 OS=Homo sapiens FALSE GN=H2AFY PE=1 SV=4 1 1 Coronin-1A GS=Homo sapiens GN=COR01A PE=1 FALSE SV=4 5 2 1 10 CTP synthase 1 OS=Homo sapiens GN=CTPS1 TRUE PE=1 SV=2 1 Culiin-associated NEDD8-dissociated protein 1 TRUE OS=Homo sapiens GN=CAND1 PE=1 SV=2 1 1 Cyc!in-dependent kinase 6 OS=Homo sapiens TRUE GN=CDK6 PE=1 SV=1 1 2 Cyclin-dependent kinase 9 OS=Homo sapiens TRUE GN=CDK9 PE=1 SV=3 1 1 Cyclin-G-associated kinase OS=Homo sapiens FALSE GN=GAK PE=1 SV=2 1 1 Cytochrome b5 type B OS=Homo sapiens FALSE GN=CYB5B PE=1 SV=2 1 1 Cytochrome c oxidase SLfbunit 4 isoform , mitochondrial OS=Homo sapiens GN=CQX411 PE=1 FALSE SV=1 1 1

Cytochrome c oxidase subunit 7A2, mitochondrial TRUE OS=Homo sapiens GN=COX7A2 PE=1 SV=1 Cytoplasmic dynein 1 heavy chain 1 OS=Homo TRUE sapiens GN=DYNC1 H 1 PE=1 SV=5 Cytoskeleton-associated protein 5 OS=Homo TRUE sapiens GN=CKAP5 PE=1 SV=3 1 Cytosoi aminopeptidase OS=Homo sapiens .F.ALSE GN=LAP3 PE=1 SV=3 D-3-phosphogiycerate dehydrogenase OS=Homo FALSE sapiens GN=PHGDH PE=1 SV=4 2 1 Deita-1-pyrroline-5-carboxyiate synthase OS Hom TRUE sapiens GN=ALDH18A1 PE=1 SV=2 Delia(3,5)-Delta(2,4)-dienoy!-CoA isornerase, mitochondrial GS=Homo sapiens GN=ECH1 PE=1 FALSE SV=2 1 1 5 Dihydrolipoyl dehydrogenase, mitochondria! FALSE OS=Homo sapiens GN=DLD PE=1 SV=2 Dipeptidyl peptidase 1 OS=Homo sapiens TRUE GN=CTSC PE=1 SV=2 1 DNA damage-binding protein 1 OS=Homo sapiens TRUE GN=DDB1 PE=1 SV=1 1 1 DNA iigase 3 OS=Homo sapiens GN=LiG3 PE=1 TRUE SV=2 1 DNA polymerase delta catalytic subunit OS=Homo TRUE sapiens GN=POLD1 PE=1 SV=2 1 3 DNA polymerase subunit gamma- 1 OS=Homo TRUE sapiens GN=POLG PE=1 SV=1 1 1 2 DNA replication licensing factor CM2 OS=Homo FALSE sapiens GN= C 2 PE=1 SV=4 1 1 DNA replication licensing factor CM3 OS=Homo FALSE sapiens GN= C 3 PE=1 SV 3 1 1 DNA replication licensing factor C 4 OS^Horno TRUE sapiens GN= C 4 PE=1 SV=5 2 1 4 DNA replication licensing factor C 5 OS=Homo TRUE sapiens GN=MCM5 PE=1 SV=5 1 1 2 DNA replication licensing factor C 6 OS^Homo TRUE sapiens GN= C 6 PE=1 SV=1 1 1 DNA replication licensing factor C 7 OS^Homo

DNA topoisomerase 1 OS=Homo sapiens

DNA topoisomerase 2-beta OS=Homo sapiens TRUE GN=TOP2B PE=1 SV=3 1 1 DNA-binding protein Ikaros OS=Homo sapiens TRUE GN=IKZF1 PE=1 SV=1 1 DNA-dependent protein kinase catalytic subunit TRUE OS=Homo sapiens GN=PRKDC PE=1 SV=3 5

DNA-directed RNA polymerase subunit RPB1 1-b1 TRUE OS=Homo sapiens GN=POLR2J2 PE=1 SV=2 Dolichyl-diphosphooligosaccharide-protein glycosyliransferase 48 kDa subunit OS=Homo TRUE sapiens GN=DDOST PE=1 SV=4 Dolichyl-diphosphooligosaccharide-protein glycosyliransferase subunit 1 OS=Homo sapiens TRUE GN=RPN1 PE=1 SV=1 11 Dolichyl-diphosphooligosaccharide-protein glycosyliransferase subunit 2 GS=Homo sapiens TRUE GN=RPN2 PE=1 SV=3 Dolichyl-diphosphooligosaccbaride-protein glycosyliransferase subunit STT3B OS=Horno TRUE sapiens GN=STT3B PE=1 SV=1 E3 ubiquitin-proiein ligase BRE1A OS=Homo TRUE sapiens GN=RNF20 PE=1 SV=2 E3 ubiquitin-proiein ligase TRAF7 OS=Homo TRUE sapiens GN=TRAF7 PE=1 SV=1 E3 ubiquitin-proiein ligase UBR5 OS=Homo sapiens TRUE GN=UBR5 PE=1 SV=2 E3 ubiquitin/ISG15 ligase T RI 25 OS=Homo TRUE sapiens GN T R 25 PE=1 SV 2 ELAV-iike protein 1 OS=Homo sapiens GN=ELAVL1 FALSE PE=1 SV=2 Electron transfer flavoprotein subunit alpha, mitochondrial OS=Homo sapiens GN=ETFA PE=1 TRUE SV=1 Elongation factor -alpha 1 OS=Homo sapiens FALSE GN=EEF1A1 PE=1 SV=1 17 Elongation factor -delta OS=Homo sapiens TRUE GN=EEF1D PE=1 SV=5 1 Elongation factor -gamma OS=Homo sapiens FALSE GN=EEF1G PE=1 SV=3 1 4 Elongation factor 2 OS=Homo sapiens GN=EEF2 FALSE PE=1 SV=4 3 2 1 Elongation factor G , mitochondria! OS-Homo FALSE sapiens GN=GFM1 PE=1 SV=2 1 Elongation factor Tu, mitochondrial OS=Homo FALSE sapiens GN=TUF PE=1 SV=2

FALSE

FALSE Eukaryotic translation initiation factor 2 subunit 1 TRUE OS=Homo sapiens GN=EIF2S1 PE=1 SV=3 Eukaryotic translation initiation factor 3 subunit C- iike protein OS=Homo sapiens GN=EIF3CL PE=3 TRUE SV=1 1 Eukaryotic translation initiation factor 3 subunit F TRUE OS=Homo sapiens GN=E!F3F PE=1 SV=1 9 Eukaryotic translation initiation factor 3 subunit TRUE OS=Homo sapiens GN=E!F3I PE=1 SV=1 Eukaryotic translation initiation factor 4 gamma 2 TRUE OS=Homo sapiens GN=EIF4G2 PE=1 SV=1 1 Eukaryotic translation initiation factor 5 OS=Homo FALSE sapiens GN=EIF5 PE=1 SV=2 2 Eukaryotic translation initiation factor 5A-1 FALSE OS^Homo sapiens GN=EIF5A PE=1 SV=2 Ezrin OS=Homo sapiens GN=EZR PE=1 SV=4 TRUE F-actin-capping protein subunit a pha- OS=Homo TRUE sapiens GN=CAP2A1 PE=1 SV=3 F-actin-capping protein subunit alpha-2 OS=Homo TRUE sapiens GN=CAP2A2 PE=1 SV=3 1 F-actin-capping protein subunit beta OS=Homo TRUE sapiens GN=CAPZB PE=1 SV=4 1 FACT complex subunit SPT16 GS=Homo sapiens TRUE GN=SUPT18H PE=1 SV=1 1 Far upstream element-binding protein 2 OS=Homo FALSE sapiens GN=KHSRP PE=1 SV=4 7 Fatty acid synthase OS=Homo sapiens GN=FASN TRUE PE=1 SV=3 1 Fermitin family homo!og 3 OS=Homo sapiens TRUE GN=FERMT3 PE=1 SV=1 1 Focadhesin OS=Homo sapiens GN=FOCAD PE=1 TRUE SV=1 Fructose-bisphosphate aldolase A OS=Homo FALSE sapiens GN=ALDOA PE=1 SV=2 2 4 3 12 G-rich sequence factor 1 OS=Homo sapiens FALSE GN=GRSF1 PE=1 SV=3 1 1 G2/mitotic-specific cyclin-B1 OS=Homo sapiens TRUE GN=CCNB1 PE=1 SV=1 1 Gamma-interferon-inducible protein 16 OS=Homo FALSE sapiens GN=!FM6 PE=1 SV=3 1 4 Glucose-6-phosphate isomerase OS=Homo sapiens FALSE GN=GPI PE=1 SV=4 2 3 1 8 Glutamate dehydrogenase , mitochondrial TRUE OS=Homo sapiens GN=GLUD1 PE=1 SV=2 1 1 2 Glutamate receptor ionotropic, NMDA 2C OS=Homo FALSE sapiens GN=GRIN2C PE=1 SV=3 1 1 Glutamine-fructose-6-phosphate aminotransferase [isomerizing] 2 OS=Homo sapiens GN=GFPT2 TRUE PE=1 SV=3 1 Glutamine-tRNA ligase OS=Homo sapiens FALSE GN=QARS PE=1 SV=1 1 1 Glutaryl-CoA dehydrogenase, mitochondrial FALSE OS=Homo sapiens GN=GCDH PE=1 SV=1 1 1 Glutathione S-transferase P GS=Homo sapiens FALSE GN=GSTP1 PE=1 SV=2 2 3 1 8 Giyceraldehyde-3-phosphate dehydrogenase F A ! OS=Homo sapiens GN=GAPDH PE=1 SV=3 10 9 6 3 1 Glycine-tRNA ligase OS=Homo sapiens GN=GARS PE=1 SV=3 1 1 2 S G P synthase [glutamine-hydrolyzing] OS=Homo FALSE sapiens GN G PS PE=1 SV=1 1 1 Growth factor receptor-bound protein 2 OS=Homo TRUE sapiens GN=GRB2 PE=1 SV=1 1 1 GTP-binding nuclear protein Ran OS=Homo sapiens TRUE GN=RAN PE=1 SV=3 2 4 7

Guanine nucleotide-binding protein G(q) subunit TRUE alpha OS=Homo sapiens GN=GNAQ PE=1 SV=4 1 2 Heat shock 70 kDa protein 4 OS=Homo sapiens FALSE GN=HSPA4 PE=1 SV=4 1 1 Heat shock 70 kDa protein 6 OS=Homo sapiens FALSE GN=HSPA6 PE=1 SV=2 1 1 1 3 Heat shock cognate 7 1 kDa protein OS=Homo FALSE sapiens GN=HSPA8 PE=1 SV=1 1 3 2 6 Heat shock protein 75 kDa, mitochondrial OS=Homo FALSE sapiens GN=TRAP1 PE=1 SV=3 2 1 1 6 Heat shock protein HSP 90-aipha OS=Homo FALSE sapiens GN=HSP90AA1 PE=1 SV=5 9 6 6 25 Heat shock protein HSP 90-beta OS=Homo sapiens FALSE GN=HSP90AB1 PE=1 SV=4 8 7 3 25 Heat shock-related 70 kDa protein 2 OS=Homo FALSE sapiens GN=HSPA2 PE=1 SV=1 1 1 2 5 Hemoglobin subunit epsilon OS=Homo sapiens TRUE GN=HBE1 PE=1 SV=2 1 1 Heterogeneous nuclear ribonudeoprotein A/B TRUE OS=Homo sapiens GN=HNRNPAB PE=1 SV=2 1 1 Heterogeneous nuclear ribonudeoprotein A O TRUE OS=Homo sapiens GN=HNRNPA0 PE=1 SV=1 2 Heterogeneous nuclear ribonudeoprotein A 1 FALSE OS=Homo sapiens GN=HNRNPA1 PE=1 SV=5 7 1 1 10 Heterogeneous nuclear ribonudeoprotein D O TRUE OS=Homo sapiens GN=HNRNPD PE=1 SV=1 1 2 Heterogeneous nuclear ribonudeoprotein H FALSE OS=Homo sapiens GN=HNRNPH1 PE=1 SV 4 5 4 1 13 Heterogeneous nuclear ribonudeoprotein H3 TRUE OS=Homo sapiens GN=HNRNPH3 PE=1 SV=2 1 Heterogeneous nuclear ribonudeoprotein K FALSE OS=Homo sapiens GN=HNRNPK PE=1 SV=1 7 Heterogeneous nuclear ribonudeoprotein L FALSE OS=Homo sapiens GN=HNRNPL PE=1 SV=2 1 Heterogeneous nuclear ribonudeoprotein M TRUE OS=Homo sapiens GN=HNRNPM PE=1 SV=3 Heterogeneous nuclear ribonudeoprotein Q TRUE OS=Homo sapiens GN=SYNCRIP PE=1 SV=2 1 Heterogeneous nuclear ribonudeoprotein R TRUE OS=Homo sapiens GN=HNRNPR PE=1 SV=1 1 Heterogeneous nuclear ribonudeoprotein U TRUE OS=Homo sapiens GN=HNRNPU PE=1 SV=6

Heterogeneous nuclear ribonucleoproteins A2/B1 FALSE OS=Homo sapiens GN=HNRNPA2B1 PE=1 SV=2 11 Heterogeneous nuclear ribonucleoproteins C1/C2 FALSE OS=Homo sapiens GN=HNRNPC PE=1 SV=4 2 7 High mobility group protein B 1 OS=Homo sapiens FALSE G =H GB1 PE=1 SV=3 1 1 Histone deacetylase 6 OS=Homo sapiens TRUE GN=HDAC6 PE=1 SV=2 1 2 Histone H1.3 OS=Homo sapiens GN=HIST1 H FALSE PE=1 SV=2 1 1 Histone H1.5 OS=Homo sapiens GN=HIST1 H B FALSE PE=1 SV=3 3 Histone H2A type 1-B/E OS=Homo sapiens FALSE GN=HIST1 H2AB PE=1 SV=2 3 3 17 Histone H2A type 2-A OS=Homo sapiens FALSE GN=HIST2H2AA3 PE=1 SV 3 1 1 Histone H2A type 2-B OS=Homo sapiens FALSE GN=HIST2H2AB PE=1 SV=3 3 2 12 Histone H2A OS=Homo sapiens GN=H2AFJ PE FALSE SV=1 1 1 Hisione H2A.V OS=Horno sapiens GN=H2AFV FALSE PE=1 SV=3 3 3 3 13 Histone H2B type 2-F OS=Homo sapiens FALSE GN=HIST2H2BF PE=1 SV=3 4 5 1 20 Histone H2B type 3-B OS=Homo sapiens TRUE GN=HIST3H2BB PE=1 SV=3 1 Histone H3.2 OS=Homo sapiens GN=H!ST2H3A TRUE PE=1 SV=3 Histone H3.3 OS=Homo sapiens GN=H3F3A PE=1 FALSE SV=2 1 4 Histone H4 OS=Homo sapiens GN=H!ST1 H4A FALSE PE=1 SV=2 5 6 5 20 Histone-lysine N-methy!transferase S YD3 TRUE OS=Homo sapiens GN=SMYD3 PE=1 SV=4 1 Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial GS=Homo sapiens GN=HADH PE=1 TRUE SV=3 1 3 Hypoxia up-regulated protein 1 OS=Homo sapiens FALSE GN=HYOU1 PE=1 SV=1 3 2 2 10 portin SLfbunit aipha-1 OS=Homo sapiens TRUE GN=KPNA2 PE=1 SV=1 1 1 Imporiin SLfbunit beta-1 OS=Homo sapiens FALSE GN=KPNB1 PE=1 SV=2 1 3 2 7

TRUE lmportin-4 OS=Homo sapiens GN=iP04 PE=1 SV=2 2 2

TRUE lmportin-9 OS=Homo sapiens GN=IP09 PE=1 SV=3 1 3 lnosine-5'-monophosphate dehydrogenase 2 TRUE OS^Homo sapiens G =I PDH2 PE=1 SV=2 2 2 Interleukin enhancer-binding factor 2 OS=Homo TRUE sapiens GN=ILF2 PE=1 SV=2 1 Interleukin enhancer-binding factor 3 OS=Homo FALSE sapiens GN=ILF3 PE=1 SV=3 Isocitrate dehydrogenase [NADP], mitochondrial FALSE OS=Homo sapiens GN=IDH2 PE=1 SV=2 Keratin, type ! cytoskeletai 7 OS=Homo sapiens TRUE G KRT7 PE=1 SV=5 1 Kinetochore protein Spc24 OS=Horno sapiens TRUE GN=SPC24 PE=1 SV=2 1 L-lactate dehydrogenase A chain OS=Homo sapiens FALSE GN=LDHA PE=1 SV=2 4 5 18 L-lactate dehydrogenase A-like 6B OS=Homo FALSE sapiens GN=LDHAL6B PE=1 SV=3 1'1' L-lactate dehydrogenase B chain OS=Homo sapiens FALSE GN=LDHB PE=1 SV=2 14 Lamin-B receptor OS= Homo sapiens GN=LBR TRUE PE=1 SV=2 1 Lamin-B1 OS=Homo sapiens GN=LMNB1 PE=1 TRUE SV=2 17 Lamina-associated polypeptide 2 , isoforms beta/gamma OS=Homo sapiens GN=TMPO PE=1 FALSE SV=2 9

Large neutral amino acids transporter small subunit FALSE 1 OS=Homo sapiens GN=SLC7A5 PE=1 SV=2 3 Leucine-tRNA ligase, cytoplasmic OS=Homo FALSE sapiens GN=LARS PE=1 SV=2 1 Lon protease homolog, mitochondrial GS=Homo TRUE sapiens GN=LGNP1 PE=1 SV=2 2 Long-chain-fatty-acid-CoA ligase 4 OS=Homo TRUE sapiens GN=ACSL4 PE=1 SV=2 1 Lymphocyte cytosolic protein 2 QS=Homo sapiens TRUE GN=LCP2 PE=1 SV=1 1 Lymphoid enhancer-binding factor 1 OS=Homo TRUE sapiens GN=LEF1 PE=1 SV=1 Macrophage migration inhibitory factor OS=Homo FALSE sapiens GN=MIF PE=1 SV=4 1 3 1 7 Magnesium transporter protein 1 OS=Homo sapiens TRUE GN AGT 1 PE=1 SV=1 1 1 Malate dehydrogenase, mitochondrial OS=Homo FALSE sapiens GN= DH2 PE=1 SV=3 3 2 4 13 TRUE Malectin OS=Homo sapiens GN=MLEC PE=1 SV=1 1 a rin-3 OS=Homo sapiens GN ATR3 PE=1 FALSE SV=2 3 2 1 10 Medium-chain specific acyi-CoA dehydrogenase, mitochondrial OS=Homo sapiens GN=ACADM PE=1 FALSE SV=1 1 1 2 Meiotic nuclear division protein 1 homolog TRUE OS=Homo sapiens GN=MND1 PE=1 SV=1 1 1 Membrane-associated progesterone receptor component 1 OS=Homo sapiens GN=PGRMC1 FALSE PE=1 SV=3 1 1 Membrane-associated progesterone receptor component 2 OS=Homo sapiens GN=PGRMC2 TRUE PE=1 SV=1 1 1 2 Metaxin-1 OS=Homo sapiens GN=MTX1 PE=1 FALSE SV=2 1 1 Methionine-tRNA ligase, cytoplasmic OS=Homo TRUE sapiens GN=MARS PE=1 SV=2 1 1 MICOS complex subunit MIC60 GS=Homo sapiens FALSE GN=IMMT PE=1 SV=1 1 1 Mitochondrial dicarboxyiate carrier OS=Homo TRUE sapiens GN=SLC25A10 PE=1 SV=2 1 1 Mitochondrial import inner membrane translocase subunit TIM44 OS=Homo sapiens G TI M44 TRUE PE=1 SV=2 Mitochondrial import receptor subunit TO 22 homolog OS=Homo sapiens GN=TOMM22 PE=1 TRUE SV=3 1 Mitochondrial-processing peptidase subunit alpha OS=Homo sapiens GN=PMPCA PE=1 SV=2 3 1 5 R U Mitotic checkpoint protein BUB3 OS=Homo sapiens GN=BUB3 PE=1 SV=1 1 2 R U . FALSE Moesin OS=Homo sapiens GN MS PE=1 SV=3 Multifunctional protein ADE2 OS=Homo sapiens TRUE GN=PAICS PE="i SV=3 Myosin light polypeptide 6 OS=Homo sapiens FALSE GN=MYL6 PE=*1 SV=2 1 Myosin-10 OS=Horno sapiens GN YH10 PE=1 FALSE SV=3 Myosin-1 OS=Homo sapiens GN=MYH1 PE=1 FALSE SV=3

FALSE Myosin-9 OS=Homo sapiens GN=MYH9 PE=1 SV=4 14 9 4 1 NAD-dependent malic enzyme, mitochondrial FALSE OS=Homo sapiens GN=ME2 PE=1 SV=1 1 1 NAD(P) transhydrogenase, mitochondrial OS=Homo TRUE sapiens GN=NNT PE=1 SV=3 1 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 OS=Homo sapiens TRUE GN=NDUFA13 PE=1 SV=3 1 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9 , mitochondrial OS=Homo TRUE sapiens GN=NDUFA9 PE=1 SV=2 Neutral alpha-glucosidase AB OS=Homo sapiens FALSE GN=GANAB PE=1 SV=3 Nuclear autoantigenic sperm protein OS=Homo FALSE sapiens GN=NASP PE=1 SV=2 Nuclear mitotic apparatus protein 1 OS=Homo FALSE sapiens GN=NUMA1 PE=1 SV=2 1 Nuclear receptor coactivator 5 OS=Homo sapiens TRUE G NC A5 PE=1 SV=2 Nucleobindin-2 GS=Homo sapiens GN=NUCB2 TRUE PE=1 SV=2 Nucleolar complex protein 4 homolog QS=Homo TRUE sapiens GN=NOC4L PE=1 SV=1 Nucleolar protein 58 OS=Homo sapiens GN=NOP58 TRUE PE=1 SV=1 Nucleolar protein 6 OS=Homo sapiens GN=NOL6 FALSE PE=1 SV=2 Nucleolar RNA helicase 2 OS=Homo sapiens TRUE GN=DDX2 1 PE= 1 SV=5

FALSE Nucieolin OS=Homo sapiens G!\I=NCL PE= 1 SV=3 2 5 Nucleolysin TIA-1 isoform p40 OS=Homo sapiens TRUE GN=TIA1 PE= 1 SV=3 1 1 Nucieophosmin OS=Homo sapiens GN=N PIVi 1 TRUE PE= 1 SV=2 Nudeoporin NUP 88 homoiog OS=Homo sapiens TRUE GN=NUP1 88 PE= 1 SV= 1 1 1 Nucleoprotein TPR OS=Homo sapiens GN=TPR TRUE PE= 1 SV=3 1 2 Nucleoside diphosphate kinase B OS=Homo FALSE sapiens G N= E2 PE= 1 SV=1 1 1 Nuc!eosome assembly protein 1-like 1 OS= Homo FALSE sapiens GN=NAP1 L 1 PE= 1 SV= 1 2 Nucieosome assembly protein 1-like 4 08= Homo FALSE sapiens GN=NAP1 L4 PE= 1 SV= 1 3 1 5 Peptidyi-pro!y! cis-trans isomerase A OS=Homo FALSE sapiens GN=PPiA PE= 1 SV=2 1 3 5 1 10 Peptidyl-prolyl cis-trans isomerase FKBP4 FALSE OS=Homo sapiens GN= FKBP4 PE= 1 SV=3 1 1 Peptidyl-prolyl cis-trans isomerase FKBP8 TRUE OS=Homo sapiens GN= FKBP8 PE= 1 SV=2 1 1 Peptidyi-tRNA hydrolase 2 , mitochondrial OS=Homo FALSE sapiens GN=PTRH2 PE= 1 SV= 1 1 1 Peroxiredoxin-1 OS=Homo sapiens GN= PRDX 1 FALSE PE= 1 SV= 1 1 3 2 2 9 Peroxiredoxin-2 OS=Homo sapiens GN= PRDX2 TRUE PE= 1 SV=5 Peroxisomal multifLfnctional enzyme type 2 TRUE OS=Homo sapiens G = HSD1 7B4 PE= 1 SV=3 1 Phosphate carrier protein, mitochondriai OS=Homo FALSE sapiens GN=SLC25A3 PE= 1 SV=2 0 Phosphatidylinositol 5-phosphate 4~kinase type-2 FALSE alpha OS=Homo sapiens GN=PIP4K2A PE=1 SV=2 1 Phosphatidylinositol giycan anchor biosynthesis class U protein OS=Homo sapiens GN=PIGU PE=1 TRUE SV=3 2 Phosphoglycerate kinase 1 OS=Homo sapiens FALSE GN=PGK1 PE=1 SV 3 Phosphoglycerate mutase 1 GS=Homo sapiens TRUE GN=PGAM1 PE=1 SV=2 1 Phosphoribosyl pyrophosphate synthase-associated protein 2 OS=Homo sapiens GN=PRPSAP2 PE=1 FALSE SV=1 1 TRUE Plastin-1 OS=Homo sapiens GN=PLS1 PE=1 SV=2 1 FALSE Plastin-2 OS=Homo sapiens GN=LCP1 PE=1 SV=6 Platelet-activating factor acetyihydrolase IB subunit beta OS=Homo sapiens GN=PAFAH1B2 PE=1 FALSE SV=1 Platelet-activating factor acetyihydrolase IB subunit gamma OS=Homo sapiens GN=PAFAH1 B3 PE=1 FALSE SV=1 1 Poly [ADP-ribose] polymerase 1 OS=Homo sapiens TRUE GN=PARP1 PE=1 SV=4 1 Polypyrimidine tract-binding protein 1 OS=Homo FALSE sapiens GN=PTBP1 PE=1 SV=1 1 Polypyrimidine tract-binding protein 2 OS=Homo FALSE sapiens GN=PTBP2 PE=1 SV=1 POTE ankyrin domain family member J OS=Homo FALSE sapiens GN=POTEJ PE=3 SV=1 PRA1 family protein 2 OS=Homo sapiens FALSE GN=PRAF2 PE=1 SV=1 Pre-mRNA-processing factor 6 OS=Homo sapiens TRUE GN=PRPF6 PE=1 SV=1 1 Pre-mRNA-processing-splicing factor 8 OS=Homo TRUE sapiens GN=PRPF8 PE=1 SV=2 Pre-mRNA-splicing factor ATP-dependeni RNA helicase DHX15 OS=Homo sapiens GN=DHX15 TRUE PE=1 SV=2 pre-rRNA processing protein FTSJ3 OS=Homo TRUE sapiens GN=FTSJ3 PE=1 SV=2 1 1 Probable ATP-dependent RNA helicase DDX17 TRUE OS=Homo sapiens GN=DDX17 PE=1 SV=2 1 2 1 4 Probable ATP-dependent RNA helicase DDX5 TRUE OS=Homo sapiens GN=DDX5 PE=1 SV=1 1 3 2 7

FALSE Profilin-1 OS=Homo sapiens GN=PFN1 PE=1 SV=2 5 6 4 18 TRUE Prohibitin OS=Homo sapiens GN=PHB PE=1 SV=1 Prohibitin-2 OS=Homo sapiens GN=PHB2 PE=1 TRUE SV=2 Proteasome activator complex subunit 1 OS^Homo FALSE sapiens GN=PSME1 PE=1 SV=1 1 Proteasome activator complex subunit 2 OS=Homo TRUE sapiens GN=PSME2 PE=1 SV=4 5 Proteasome subunit alpha type-4 OS=Homo sapiens FALSE G =PS A4 PE=1 SV=1 1 Proteasome subunit alpha type-7 OS=Homo sapiens FALSE G =PS A7 PE=1 SV=1 1 Proteasome subunit beta type-6 OS=Homo sapiens FALSE G =PS B6 PE=1 SV=4 2 Proteasome subunit beta type-7 OS=Homo sapiens TRUE GN=PSMB7 PE=1 SV=1 2 Protein CutA OS=Homo sapiens GN=CUTA PE=1 FALSE SV=2 1 Protein degiycase DJ-1 OS=Homo sapiens FALSE GN=PARK7 PE=1 SV=2 Protein diaphanous homo!og 1 OS=Homo sapiens FALSE GN=DIAPH1 PE=1 SV=2 1 1 Protein disulfide-isomerase A3 OS=Horno sapiens FALSE GN=PD!A3 PE=1 SV=4 1 Protein disulfide-isomerase A4 OS=Horno sapiens TRUE G PD A4 PE=1 SV=2 3 Protein disulfide-isomerase A6 OS=Homo sapiens TRUE GN=PDIA6 PE=1 SV=1 3 Protein disulfide-isomerase OS=Homo sapiens FALSE GN=P4HB PE=1 SV=3 1 2 4 Protein ERGiC-53 OS=Homo sapiens GN=LMAN1 TRUE PE=1 SV=2 1 1 Protein fem-1 homolog A OS=Homo sapiens FALSE GN=FEM1A PE=1 SV=1 1 1 Protein flightless- 1 homolog OS=Homo sapiens FALSE GN=FLII PE=1 SV=2 1 1 5 Protein LYRIC OS=Homo sapiens GN=MTDH PE=1 TRUE SV=2 1 1 Protein phosphatase 1 regulatory subunii 3E TRUE OS=Homo sapiens GN=PPP1R3E PE=1 SV=2 1 Protein RCC2 OS=Homo sapiens GN=RCC2 PE=1 TRUE SV=2 1 Protein-methionine sulfoxide oxidase MICAL1 TRUE OS=Homo sapiens GN=MICAL1 PE=1 SV=2 1 Puromycin-sensitive aminopeptidase OS=Homo TRUE sapiens GN=NPEPPS PE=1 SV=2 1 1 2 Putative beta-actin-like protein 3 OS=Homo sapiens FALSE GN=POTEKP PE=5 SV=1 3 2 1 8

Putative heat shock protein HSP 90-alpha A5 FALSE OS=Homo sapiens GN=HSP90AA5P PE=2 SV=1 1 1 1 3 Pyruvate carboxylase, mitochondrial OS=Homo TRUE sapiens GN=PC PE=1 SV=2 1 2

Pyruvate kinase PKM OS=Homo sapiens GN=PKM ∆ PE=1 SV=4 23 16 17 67 Rab GDP dissociation inhibitor beta GS=Homo FALSE sapiens GN=GDI2 PE=1 SV=2 5 5 3 16 FALSE Radixin OS=Homo sapiens GN=RDX PE=1 SV=1 3 2 5

Ras-reiated protein Rab~10 OS=Homo sapiens TRUE GN=RAB10 PE=1 SV=1 1 Ras-reiated protein Rab-1 1A OS=Homo sapiens TRUE GN=RAB1 PE=1 SV=3 2 1 3 Ras-re!ated protein Rab-1 1B OS=Homo sapiens TRUE GN=RAB1 B PE=1 SV=4 1 1 Ras-re!ated protein Rab-1 B OS=Homo sapiens FALSE GN=RAB1 B PE=1 SV=1 1 1 3 Ras-re!ated protein Rab-7a OS=Homo sapiens TRUE GN=RAB7A PE=1 SV=1 1 Ras-re!ated protein Rap-1b-like protein OS=Homo TRUE sapiens PE=2 SV=1 1 1 2 4 Receptor of activated protein C kinase 1 OS=Homo FALSE sapiens GN=RACK1 PE=1 SV=3 1 Receptor-type tyrosine-protein phosphatase C TRUE OS=Homo sapiens GN=PTPRC PE=1 SV=2 1 2 Replication factor C subunit 1 OS=Homo sapiens TRUE GN=RFC1 PE=1 SV=4 1 Reticulon-4 OS=Homo sapiens GN=RTN4 PE=1 FALSE SV=2 1 Retinoblasioma-associated protein OS=Homo TRUE sapiens GN=R81 PE=1 SV=2 1 Rho GDP-dissociation inhibitor 1 OS=Homo sapiens , FALSE GN=ARHGDIA PE=1 SV=3 1 Rho GDP-dissociation inhibitor 2 OS=Homo sapiens FALSE GN=ARHGDIB PE=1 SV=3 3 Rho guanine nucleotide exchange factor 2 TRUE OS^Homo sapiens GN=ARHGEF2 PE=1 SV=4 1 1 Rho-related GTP-binding protein RhoG OS=Homo TRUE sapiens GN=RHOG PE=1 SV=1 1 Ribosome biogenesis protein BOP1 OS=Homo FALSE sapiens GN=BOP1 PE=1 SV=2 RING finger protein 37 OS=Homo sapiens FALSE GN=UBOX5 PE=1 SV=1 RNA-binding protein 28 OS=Homo sapiens TRUE GN=RBM28 PE=1 SV=3 RNA-binding protein FUS OS=Horno sapiens TRUE GN=FUS PE=1 SV=1 RRP12-like protein OS=Homo sapiens GN=RRP12 TRUE PE=1 SV-2 RuvB-like 1 OS=Homo sapiens GN=RUVBL1 PE=1 TRUE SV=1 S-adenosy!methionine synthase isoform type-1 FALSE OS=Homo sapiens GN=MAT1A PE=1 SV=2 S-formylglutathione hydrolase OS=Homo sapiens TRUE GN=ESD PE=1 SV=2

Saccharopine dehydrogenase-like oxidoreductase TRUE OS=Homo sapiens GN=SCCPDH PE=1 SV=1 Sarcoplasmic/endoplasmic reticLflum calcium ATPase 1 OS^Homo sapiens GN=ATP2A1 PE=1 TRUE SV=1 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 OS=Homo sapiens GN=ATP2A2 PE=1 TRUE SV=1 Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 OS=Homo sapiens GN=ATP2A3 PE=1 TRUE SV=2 1 Serine hydroxymethyltransferase, mitochondrial FALSE OS=Homo sapiens GN SH T2 PE=1 SV=3 Serine palmitoyltransferase 2 0 =Homo sapiens TRUE GN=SPTLC2 PE=1 SV=1 4 Serine-tRNA iigase, cytoplasmic OS=Homo sapiens FALSE GN=SARS PE=1 SV=3 Serine/argi nine-rich splicing factor 0 OS=Homo FALSE sapiens GN=SRSF10 PE=1 SV=1 Serine/arginine-rich splicing factor 3 OS=Homo FALSE sapiens GN=SRSF3 PE=1 SV=1 3 1 5 Serine/arginine-rich splicing factor 8 OS=Homo TRUE sapiens GN=SRSF8 PE=1 SV=1 1 1 Serine/arginine-rich splicing factor 9 OS=Homo TRUE sapiens GN=SRSF9 PE=1 SV=1 2 1 3 Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform OS=Homo TRUE sapiens GN=PPP2R2D PE=2 SV=1 2 Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform OS=Homo FALSE sapiens GN=PPP2R1A PE=1 SV=4 2 Siderof!exin-1 OS=Homo sapiens GN=SFXN1 PE=1 TRUE SV=4 1

Signal peptidase complex catalytic subunit SEC1 1A TRUE OS^Homo sapiens GN=SEC1 1A PE=1 SV=1 3 Signal recognition particle subunit SRP68 OS=Homo TRUE sapiens GN=SRP88 PE=1 SV=2 Signal transducer and activator of transcription 1- alpha/beta GS=Homo sapiens GN=STAT1 PE=1 TRUE SV=2 3 2 7 Signal transducer and activator of transcription 3 TRUE OS=Homo sapiens G =STATS PE=1 SV=2 1 3 Small integral membrane protein 10-like protein 1 FALSE OS=Homo sapiens G S ! 10L1 PE=3 SV=1 1 1 Small nuclear ribonucleoprotein S D 1 OS=Homo FALSE sapiens GN=SNRPD1 PE=1 SV=1 3 3 2 14 Small nuclear ribonucleoprotein Sm D3 OS=Homo FALSE sapiens GN=SNRPD3 PE=1 SV=1

Small nuclear ribonucleoprotein-associated protein FALSE N OS=Homo sapiens GN=SNRPN PE=1 SV=1 Sodium/potassium-transporting ATPase subunit alpha-1 OS=Homo sapiens GN=ATP1A1 PE=1 TRUE SV=1 1 Soiute carrier family 2 , facilitated glucose transporter member 1 OS=Homo sapiens GN=SLC2A1 PE=1 TRUE SV=2 1 1 Solute carrier family 25 member 4 1 OS=Homo TRUE sapiens GN=SLC25A41 PE=2 SV=2 1 1 Spectrin alpha chain, non-erythrocytic 1 OS=Homo FALSE sapiens GN=SPTAN1 PE=1 SV=3 1 2 7 Spectrin beta chain, non-erythrocytic 1 OS=Homo FALSE sapiens GN=SPTBN1 PE=1 SV=2 1 1

Spermatogenesis-associated protein 5-like protein 1 TRUE OS=Homo sapiens GN=SPATA5L1 PE=1 SV=2 1 2 Spliceosome RNA heiicase DDX39B OS=Homo TRUE sapiens GN=DDX39B PE=1 SV=1 1 1 2 Splicing factor 1 OS=Homo sapiens GN=SF1 PE=1 FALSE SV=4 1 1 Splicing factor 3A subunit 1 OS=Homo sapiens FALSE GN=SF3A1 PE=1 SV=1 1 1 Splicing factor U2AF 35 kDa subunit QS=Homo FALSE sapiens GN=U2AF1 PE=1 SV=3 1 4 Splicing factor U2AF 65 kDa subunit OS=Homo TRUE sapiens GN=U2AF2 PE=1 SV=4 1 2 3 Splicing factor, proline- and glutamine-rich TRUE OS Ho o sapiens GN=SFPQ PE=1 SV=2 1 2 1 7 Stress-70 protein, mitochondrial OS=Homo sapiens TRUE GN=HSPA9 PE=1 SV=2 1 3 5 11 Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial OS=Homo sapiens FALSE GN=SDHA PE=1 SV=2 1 2 1 7 Syndecan-3 OS=Homo sapiens GN=SDC3 PE=1 SV=2 T-ce!l surface glycoprotein CD1a OS=Homo sapiens TRUE GN=CD1A PE=1 SV=4 1 T-compiex protein 1 subunit alpha OS=Homo FALSE sapiens GN=TCP1 PE=1 SV=1 3 2 9 T-comp!ex protein 1 subunii beta OS=Homo sapiens FALSE GN=CCT2 PE=1 SV=4 1 1 T-comp!ex protein 1 subunit delta OS=Homo FALSE sapiens GN=CCT4 PE=1 SV=4 3 1 1 T-comp!ex protein 1 subunit epsiion OS=Homo FALSE sapiens GN=CCT5 PE=1 SV=1 5 3 4 T-comp!ex protein 1 subunit eta OS=Homo sapiens TRUE GN=CCT7 PE=1 SV=2 T~comp!ex protein 1 subunii gamma OS=Homo TRUE sapiens GN=CCT3 PE=1 SV=4 1 3 T-comp!ex protein 1 subunii theia OS=Homo FALSE sapiens GN=CCT8 PE=1 SV=4 4 3 2 10 T-comp!ex protein 1 subunii zeia OS=Homo sapiens FALSE GN=CCT6A PE=1 SV=3 6 5 5 22 TRUE Talin-1 OS=Homo sapiens GN=TLN1 PE=1 SV=3 2 3 7 TAR DNA-binding protein 43 OS=Homo sapiens TRUE GN=TARDBP PE=1 SV=1 1 Thioredoxin-relaied transmembrane protein 1 TRUE OS=Homo sapiens GN=TMX1 PE=1 SV=1 1 1 3 Thioredoxin-relaied transmembrane protein 4 TRUE OS=Homo sapiens GN=TMX4 PE=1 SV=1 1 1 Transferrin receptor protein 1 OS=Homo sapiens TRUE GN=TFRC PE=1 SV=2 1 1 Transitional endoplasmic reticulum ATPase FALSE OS=Homo sapiens GN=VCP PE=1 SV=4 2 4 2 8 Transketoiase OS=Homo sapiens GN=T T PE=1 FALSE SV=3 4 3 3 15 Translin-associated protein X OS=Homo sapiens TRUE GN=TSNAX PE=1 SV=1 Transmembrane protein 9 OS=Homo sapiens FALSE GN=TME 09 PE=1 SV=1 Transmembrane protein 126A OS^Homo sapiens TRUE GN=TMEM126A PE=1 SV=1 Transmembrane protein 160 OS=Homo sapiens TRUE GN=T E 160 PE=1 SV=1 Transmembrane protein 33 OS=Homo sapiens TRUE G T E 33 PE=1 SV=2 Tricarboxy!ate transport protein, mitochondrial FALSE OS=Homo sapiens GN=SLC25A1 PE=1 SV=2 Trifunctlonai enzyme subunit alpha, mitochondrial TRUE OS=Homo sapiens GN=HADHA PE=1 SV 2

Trifunctlonai purine biosynthetic protein adenosine-3 FALSE OS=Homo sapiens GN=GART PE=1 SV=1 Triosephosphate isomerase OS=Homo sapiens FALSE GN=TPI1 PE=1 SV=3 3 tRNA-splicing ligase RtcB homolog OS=Homo TRUE sapiens GN=RTCB PE=1 SV=1 5 Tubulin aipha-1A chain OS=Homo sapiens FALSE GN=TUBA1A PE=1 SV=1 9 Tubulin aipha-3C/D chain OS=Homo sapiens FALSE GN=TUBA3C PE=1 SV=3 5 15 Tubulin alpha-4A chain OS=Homo sapiens TRUE GN=TUBA4A PE=1 SV=1 1 2 1 6 Tubulin beta chain OS=Homo sapiens GN=TUBB FALSE PE=1 SV=2 3 2 1 10 Tubulin beta-3 chain OS=Homo sapiens GN=TUBB3 FALSE PE=1 SV=2 10 6 8 4 34 Tubulin beta-4B chain OS=Homo sapiens FALSE GN=TUBB4B PE=1 SV=1 1 1 2 1 5 Tubulin beta-6 chain OS=Homo sapiens GN=TUBB6 FALSE PE=1 SV=1 1 2 2 1 10 Tumor necrosis factor alpha-induced protein 8 TRUE OS=Homo sapiens GN=TNFAIP8 PE=1 SV=1 1 1 2 Tyrosine-protein kinase CSK GS=Homo sapiens TRUE GN=CSK PE=1 SV=1 1 Tyrosine-protein kinase Lck OS=Homo sapiens TRUE GN=LCK PE=1 SV=6 1

U5 small nuclear ribonucleoprotein 200 kDa helicase TRUE OS=Homo sapiens G S R P200 PE=1 SV=2 Ubiquitin carboxyl-terminal hydrolase 14 OS=Homo TRUE sapiens GN=USP14 PE=1 SV=3 Ubiquitin carboxy - er na hydrolase 7 OS^Homo FALSE sapiens GN=USP7 PE=1 SV=2 Ubiquitin-60S ribosomai protein L40 OS=Horno FALSE sapiens GN=UBAS2 PE=1 SV=2 Ubiquitin-like modifier-activating enzyme 1 FALSE OS=Homo sapiens GN=UBA1 PE=1 SV=3 11 UDP-glucose:glycoprotein glucosyltransferase 1 TRUE OS=Homo sapiens GN=UGGT1 PE=1 SV=3 U P-C P kinase OS=Homo sapiens GN C PK1 FALSE PE=1 SV=3 2 3 7 Very-long-chain enoyl-CoA reductase OS=Homo TRUE sapiens GN=TECR PE=1 SV=1 1 1 Vesicle-associated membrane protein-associated protein B/C OS=Homo sapiens GN=VAPB PE=1 TRUE SV=3 1 1 Vesicle-trafficking protein SEC22b OS=Homo TRUE sapiens GN=SEC22B PE=1 SV=4 1 1

Voltage-dependent anion-selective channel protein 1 TRUE QS^Homo sapiens GN=VDAC1 PE=1 SV=2 1 1

Voltage-dependent anion-selective channel protein 2 TRUE S Ho o sapiens GN=VDAC2 PE=1 SV=2 1 1 Werner syndrome ATP-dependent helicase TRUE OS=Homo sapiens GN=WRN PE=1 SV=2 1 1 X-ray repair cross-complementing protein 5 TRUE OS=Homo sapiens GN=XRCC5 PE=1 SV=3 1 6 2 10 X-ray repair cross-complementing protein 6 OS=Homo sapiens GI\!=XRCC6 PE=1 SV=2 2 2 17 . Zinc finger protein 469 OS=Homo sapiens TRUE GN=ZNF469 PE=2 SV=3 . . .

Zinc finger protein with KRAB and SCAN domains 3 TRUE OS=Homo sapiens GN=ZKSCAN3 PE=1 SV=2 1

MSAIDs. All spectra were manually validated for the isotopic code (MS1) and spectral assignment (MS2).

Prote Treatment

[Rj.lEGLTDEINFL Keratin, type II photo- P05787 L1(CV Nap SiC2N3) 937.4829 2.56 K562 R.[Q] cytoskeletal 8 naproxen 4 [R].LEGLTDEInFL Keratin, type II photo- P05787 N9(CW_Cele__SiC2N3) 982.9542 2.48 K562 R.[Q] cytoskeletal 8 celecoxib 5 [Rj.LEGITDEINFL Keratin, type II photo- P05787 L4(CW_Cele__SiC2N3) 982.9542 2.09 K562 R.[Q] cytoskeletal 8 celecoxib 5 [KJ.LSEIEAALQR. Keratin, type photo- P05787 L4(CW__Nap_SiC2N3) 792.4207 2.67 K562 [A] cytoskeletal 8 naproxen 4 [Rj.LEGLTDelNFL Keratin, type I photo- P05787 E7(C Nap_ SiC2N3) 937.4829 3.07 K562 R.[Q] cytoskeletal 8 naproxen 4 [Rj.cEKQSPGVA C 1(Carbamidomethylj; Neuroblastoma- A2RRP1 NELLKEYLVTLAk K22(CW__minimalist__Si2N 1373.745 2.62 K562 tag 7 ampiified sequence [G] 3) Nascent polypeptide- [K].iEDLSQQAQL associated complex photo- E9PAV3 l1(C J Sap SiC2N3) 1035.025 3.88 K562 AAAEK.FF] subunit alpha, muscle- naproxen 4 specific form Nascent polypeptide- [K].iEDLSQQAQL associated complex photo- E9PAV3 l1(C J Sap SiC2N3) 1035.026 3.76 K562 AAAEK.fF] subunit alpha, muscle- naproxen 4 specific form Nascent polypeptide- [KJ.IEDISQQAQL associated complex photo- E9PAV3 L4(CW_Nap SiC2N3) 2 1035.026 1.77 K562 AAAEK.fF] subunit alpha, muscle- naproxen 4 specific form Nascent polypeptide- [K].leDLSQQAQL associated complex photo- E9PAV3 E2(CW_Nap_SiC2N3) 1035.027 3.87 Jurkat AAAEK. F subunit alpha, muscle- naproxen 4 specific form Nascent polypeptide- [K].iEDLSQQAQL associated complex photo- E9PAV3 H(CW_Nap_SiC2N3) 2 1035.027 1.51 Jurkat AAAEK.FF] subunit alpha, muscle- naproxen 4 specific form

Alkyldihydroxyacetonep [Rj.GiSDPLTVFE photo- 0001 6 l2(CW_miniGL_SiON3) hosphate synthase, 2 1107.045 2.81 Jurkat QTEAAAR.[E] glutarimide 8 peroxisomal

Unconventional myosin- photo- 000159 [R].RIGLER.[N] L2(CW_Nap_SiC0N3) 2 598.3326 1.35 K562 naproxen 4 [Rj.GELPdFQdGT D5(CW_minimalist_Si2N3 KATFHYRTLHSD ) ; AH receptor-interacting 000170 3 1379.002 1.4 K562 tag 7 DEGTVLDDSR [A D8(CW_minimalist_Si2N3 protein ] ) [R] !EEPSLRCVE photo- 000429 L1(CW_Nap_SiC2N3) Dynamin-1-like protein 1326.155 2.59 K562 LVHEEMQR.fl] naproxen 4 [KJ.YPASTVQIIGA photo- 000567 L9(CW_Cele_SiC2N3) Nucleolar protein 58 2 961 .4556 2.95 K562 EK.[A] ceiecoxib [K].MWVDRYLAF AT-rich interactive M15(Oxidation); photo- O14497 TEEKAmGMTNL domain-containing 3 1118.879 3.47 Jurkat R25(CW_Nap_SiC0N3) naproxen 4 PA Gr.[ protein 1

UDP-N- [K].eAIRISPTFAD acetylglucosamine- photo- AYSN GNTLK E E1(CW_Nap_SiC2N3) peptide N- 1377.182 2.9 K562 naproxen 4 acetylglucosaminyltrans ferase 110 kDa subunit

043175 C CW Nap S C2N3 D-3-phosphogiycerate photo- , 1012.051 2.92 K562 IVGLLK.[E] _ _ dehydrogenase naproxen [KJ.NAGnCLSPAV D-3-phosphoglycerate photo- 043175 N4(CW_Nap_SiC2N3) 2 1012.051 2.18 K562 VGLLK [E] dehydrogenase naproxen 4 26S proteasorne non- [K].LQLDSPEDAe photo- 043242 El 0(CW_Cele_SiC2N3) ATPase regulatory 2 1110.515 2.35 K562 FiVAK.[A] ceiecoxib 5 subunit 3 SWi/SNF-reiated matrix- [K].DEKqNLLSVG associated actin- photo- 060264 Q4(CW_Nap__SiC0N3) 2 994.9933 2.87 Jurkat DYR.[H] dependent regulator of naproxen chromatin subfamily A [K].TMLETEEGIIL Protein diaphanous 060610 L10(CW_Cele_SiC2N3) 2 1081 .534 1.33 K562 LVR.[A] homoiog 1 celecoxib 5 [K].QVHpDTGISS photo- 060814 P4(CW_Cele_SiC2N3) Histone H2B type 1-K 3 571 .9218 1.73 K562 K.[A] celecoxib 5

M2(Oxidation); [KJ.AmGimNSFV photo- 060814 MS(Oxidation); Histone H2B type 1-K 2 1160.986 3.28 NdlFER.[i] celecoxib 5 D 1(CW_Cele_SiC2N3)

M2(Oxsdatson); [KJ.AmGimNSFV photo- 060814 5(Oxida on); Histone H2B type 1-K 2 1160.983 4.08 NDIFEr.N] celecoxib 5 R15(CW_Cele_SiC2N3)

M2(Oxidafion); [KJ.AmGimNSFV photo- 060814 M5(Oxidation); Histone H2B type 1-K 2 1160.983 1.67 K562 NDIfER . celecoxib 5 F13(CW_Cele_SiC2

[KJ.AMGImNSFV M5(Oxidation); 060814 Histone H2B type 1-K 2 1152.988 2.94 K562 Nd!FER.[l] D 1 1(CW_Cele_SiC2N3) celecoxib 5

[K].AmGIMNSFV M2{Oxidation); photo- 060814 Histone H2B type 1-K 2 1152.989 2.62 K562 NDIFEr.[l] R15(CW_Cele_SiC2N3) celecoxib 5

[KJ.AmGIMNSFV M2(Oxidation); photo- 060814 Histone H2B type 1-K 2 1152.985 2.77 K562 NdlFER.Nl D 1 1(CW_Cele_SiC2N3) ceiecoxib 5 M2(Oxidaiion); [KJ.AmGlmNSFV photo- 060814 MSiOxidation); Hisione H2B type 1-K 2 1115.51 1 3.97 K562 NDIFEr.[l] naproxen 4 R15(CW_Nap SiC2N3)

M2(Oxidation); [KJ.AmGlmNSFV photo- 060814 M5(Oxidation); Histone H2B type 1-K 2 1115.51 1 2.66 K562 NDIFeR.[l] naproxen 4 E14(CW_Nap_SiC2N3)

[KJ.AmGlmNSFV photo- 060814 M5(Oxidation); Histone H2B type 1-K 2 1115.512 4.1 1 K562 NDIFEr.[IJ naproxen 4 R15(CW_Nap_SiC2N3) M2(Oxidaiion); [KJ.AmGlmNSFV photo- 060814 M5(Oxidaiion); Hisione H2B type 1-K 2 1115.512 2.5 K562 NDIFeR.[IJ naproxen E14(CW_Nap_SiC2N3) M2(Oxidaiion); [KJ.AmGlmNSFV photo- 060814 M5(Oxidaiion); Histone H2B type 1-K 3 744.0126 3.04 K562 NDIFeR.[l] naproxen 4 E14(CW_Nap_SiC2N3) M2(Oxidaiion); [KJ.AmGlmNSFV photo- 060814 MSiOxidation); Histone H2B type 1-K 2 1115.514 4.15 K562 NDIFeR.[l] naproxen 4 E14(CW_Nap_SiC2N3) M2(Oxidation); [KJ.AmGlmNSFV photo- 060814 M5(Oxidaiion); Histone H2B type 1-K 2 1115.514 2.39 K562 NdlFER.[IJ naproxen 4 D 1 1(CW_Nap_SiC2N3)

[KJ.AMGImNSFV M5(Oxidaiion); photo- 060814 Histone H2B type 1-K 2 1107.515 3.71 K562 NDIFEr.[IJ R15(CW_Nap_SiC2N3) naproxen 4 [KJ.AMGImNSFV MSiOxidation); photo- 060814 Histone H2B type 1-K 2 1107.515 2.76 K562 NDIFeR.[l] E14(CW_Nap_SiC2N3) naproxen 4 [KJ.AMGImNSFV M5(Oxidation); photo- 060814 Histone H2B type 1-K 2 1107.516 3.99 K562 NDIFeR.[IJ E14(CW_Nap_SiC2N3) naproxen 4 [KJ.AMGImNSFV M5(Oxidation); photo- 060814 Histone H2B type 1-K 2 1107.516 2.18 K562 NDIFeR.[l] E14(CW_Nap_SiC2N3) naproxen 4 [KJ.AmGIMNSFV M2(Oxidaiion); photo- 060814 Histone H2B type 1-K 2 1107.515 4.14 K562 NDIFEr.[IJ R15(CW_Nap_SiC2N3) naproxen 4 [KJ.AmGIMNSFV M2(Oxidation); photo- 060814 Hisione H2B type 1-K 2 1107.515 1.41 K562 NDIfER.[l] F13(CW_Nap_SiC2N3; naproxen [KJ.AmGIMNSFV M2(Oxidaiion): photo- 060814 Histone H2B type 1-K 3 738.6817 4 K562 NDIFeR.[IJ E14(CW_Nap_SiC2N3 naproxen

[KJ.AmGIMNSFV M2(Oxidation); photo- 060814 Hisione H2B type 1-K 3 738.6817 2.34 K562 NdlFER.N] D 1 1(CW_Nap_SiC2N3 naproxen

[KJ.AmGIMNSFV M2(Oxidation); photo- 060814 Histone H2B type 1-K 2 1107.514 4.54 K562 NDIFEr .m R15(CW_Nap_SiC2N3 naproxen

[KJ.AmGI 1NSFV M2(Oxidation); photo- 060814 Histone H2B type 1-K 2 1107.514 1.56 K562 Nd FER. I] D 1 1(CW_Nap_SiC2N3 naproxen

[KJ.AmGIMNSFV M2(Oxidaiion); photo- 060814 Histone H2B type 1-K 3 738.6788 3.77 K562 NDIFeR.[ J E14(CW_Nap_SiC2N3 naproxen [KJ.AmGIMNSFV M2(Oxidation); photo- 060814 Histone H2B type 1-K 3 738.6788 2.39 K562 ND FeR ': E14(CW_Nap_SiC2N3 naproxen [KJ.AmGI MNSFV photo- -4 060814 Histone H2B type 1-K 2 1107.515 2.41 K562 NDIFeR. [:i] E14(CW_Nap_SiC2N3 naproxen [KJ.AmGI 1NSFV M2(Oxidation); photo- 060814 Histone H2B type 1-K 2 1107.515 4.34 K562 NDIFEr.[l J R15(CW_Nap_SiC2N3 naproxen [KJ.AMGI MNSFV photo- 060814 R15(CW_Nap_SiC2N3 Histone H2B type 1-K 2 1099.516 2.89 K562 NDIFEr.[l ] naproxen [KJ.AMGI MNSFV photo- 060814 R15(CW_Nap SiC2N3 Histone H2B type 1-K 2 1099.516 4.25 K562 NDIFEr.[l ] naproxen [KJ.AMGI MNSFV photo- 060814 E14(CW_Nap_SiC2N3 Hisione H2B type 1-K 2 1099.516 2.45 K562 NDIFeR. naproxen

M2(Oxidation); 060814; [KJ.AmGlmNSFV M5(Oxidaiion); Histone H2B type 1-K 2 1160.985 3.3 Jurkat Ρ06899 NdlFER.Nl ceiecoxib 5 D 1 1(CW_Cele_SiC2N3)

M2(Oxidaiion); 060814; [KJ.AmGlmNSFV photo- M5(Oxidaiion); Hisione H2B type 1-K 2 1160.985 2.8 Jurkat Ρ06899 NdlFER.Nl ceiecoxib D 1 1(CW_Cele_SiC2N3) Οδθ 51 4 ; [KJ.AMGI mNSFV M5(Oxidation); photo- Histone H2E$type 1-K 2 1152.991 2.79 Jurkat Ρ 6 ί399 Ndl FER.[l] D 1 1(CW_Cele_SiC2N3) celecoxib 5

Ο 60 J1 4 ; [KJ.AMGI mNsFVN M5(Oxidation); photo- Histone H2E$type 1-K 2 1152.991 2.24 Jurkat Ρ 6 ί399 D FER. ] S7(CW__Cele__SiC2N3) celecoxib

60 1 4 ; [KJ.AmGIMNSFV M2(Oxidaiion); photo- Histone H2E$type 1-K 2 1152.99 2.67 Jurkat Ρ 06 399 Ndl FER.[l] D 1 1(CW_Cele_SiC2N3) ceiecoxib 5

Ο 60 1 4 ; [KJ.AmGIMNSFvN M2(Oxidation); photo- Histone H2EJtype 1-K 2 1 52.99 2.3 Jurkat Ρ 6 399 D IFER. [I] V9(Cwlcele_SiC2N3) celecoxib 5

[KJ.AmGlmNSFV M2(Oxidation); Ο 60 1 4 ; photo- NDI FERIAgEASR M5(Oxidation); Histone H2E$type 1-K 3 1002.443 2.48 Jurkat P 6 399 celecoxib 5 [L] G 18(CW_Cele_SiC2N3)

Οδθ $1 4 ; [KJ.QVhPDTGISS photo- H3(CW_Cele_SiC2N3) Histone H2E type 1-K 3 571 .923 2.42 Jurkat Ρ 06<399 K .[A] celecoxib 5 M2(Oxidation); photo- Ο 60 $1 4 ; [KJ.AmGimNSFV l4(CW_lndo_SiC2N3); Histone H2E$type 1-K 2 1185.52 1 2.28 Jurkat indomethacin P06?399 NDI FER. [I] M5(Oxidation) 6

M2(Oxidation); Ο 60 $1 4 ; [KJ.AmGlmNSFV photo- M5(Oxidation); Histone H2E$type 1-K 2 1115.51 2 3.2 Jurkat Ρ 6 ί399 NDI FEr. [l] naproxen 4 R 15(CW_Nap_SiC2N3)

M2(Oxidation); Ο 60 $1 4 ; [KJ.AmGlmNSFV photo- M5(Oxidation); Histone H2E$type 1-K 2 1115.51 2 2.52 Jurkat ΡΟδ 399 NDI FeR. [l] naproxen 4 E 14(CW_Nap_SiC2N3) M2(Oxidation); Ο 60 $1 4 ; [KJ.AmGlmNSFV photo- M5(Oxidaiion); Histone H2EJtype 1-K 2 1115.51 2 4.01 Jurkat P06?399 NDI FeR. [l] naproxen 4 E 14(CW_Nap_SiC2N3) M2(Oxidaiion); οβοε$1 4 ; [KJ.AmGlmNSFV photo- M5(Oxidaiion); Histone H2EJtype 1-K 2 1115.51 2 2.67 Jurkat Ρ 06 399 NDI FeR. [l] naproxen 4 E 14(CW_Nap_SiC2N3)

Ο δ 0 J1 4 ; [KJ.AMGI mNSFV M5(Oxidation); photo- Hisione H2E type 1-K 2 11 7.513 3.48 Jurkat Ρ 6 ί399 NDI FEr. [IJ R 15(CW_Nap_SiC2N3) naproxen 4 060814; [KJ.AMGImNSFV M5(Oxidation); photo- Hisione H2B type 1-K 1107.513 2.71 Jurkat P06899 NDIFeR.[l] E14(CW_Nap_SiC2N3) naproxen 4 060814; [KJ.AMGImNSFV M5(Oxiclaiion); photo- Histone H2B type 1-K 1107.517 2.74 Jurkat P06899 NDIFEr.[l] R15(CW_Nap_SiC2N3) naproxen 4 060814; [KJ.AMGImNSFV M5(Oxidation); photo- Histone H2B type 1-K 1107.517 1.76 Jurkat P06899 NDIfER.[l] F13(CW_Nap_SiC2N3) naproxen 4 060814; [KJ.AmGIMNSFV M2(Oxidaiion); photo- Histone H2B type 1-K 3 738.6818 4.07 Jurkat P06899 NDIFeR.[IJ E14(CW_Nap_SiC2N3) naproxen 4 060814; [KJ.AMGIMNSFV photo- E14(CW_Nap_SiC2N3) Histone H2B type 1-K 2 1099.517 3.85 Jurkat P06899 NDIFeR.[l] naproxen 4 060814; [KJ.AMGIMNSFV photo- E14(CW_Nap_SiC2N3) Histone H2B type 1-K 2 1099.517 1.94 Jurkat P06899 NDIFeR.[l] naproxen 4 060814; [KJ.AMGIMNSFV photo- E14(CW_Nap SiC2N3) Histone H2B type 1-K 3 733.348 3.8 Jurkat P06899 NDIFeR.[IJ naproxen 4 060814; [KJ.AMGIMNSFV photo- E14(CW_Nap_SiC2N3) Hisione H2B type 1-K 3 733.348 3.35 Jurkat P06899 NDIFeR.[l] naproxen 4 060814; [KJ.AMGIMNSFV photo- E14(CW_Nap_SiC2N3) Histone H2B type 1-K 1099.518 1.93 Jurkat P06899 NDIFeR.[l] naproxen 4 060814; [KJ.AmGIMNSFV M2(Oxidation); photo- Hisione H2B type 1-K 1107.517 2.52 Jurkat P06899 NDIFEr.[IJ R15(CW_Nap_SiC2N3) naproxen 4 060814; [KJ.AMGIMNSFV photo- R15(CW_Nap SiC2N3) Histone H2B type 1-K 1099.517 3.95 Jurkat P06899 NDIFEr.[IJ naproxen 4 060814; [KJ.AMGIMNSFV photo- E14(CW_Nap_SiC2N3) Histone H2B type 1-K 2 1099.519 2.42 Jurkat P06899 NDIFeR.[l] naproxen 4 [KJ.eELEQKCKSV Rho-associated protein 0751 6 E1(CW_lndo_SiC2N3) 2 1079.51 2.34 K562 indomethacin NTR.[LJ kinase 2

[RJ.LVSPGSANE photo- 075369 TSSiLVESVTR.FS H3(CW_Cele_SiC0N3) Filamin-B 1295.106 2.72 K562 celecoxib 5

G75694 photo- celecoxib 5 [KJ.VQqRUGFmR Q3(CW_Nap_SiC0N3); Nuclear pore complex photo- 075694 PENGNPQQmQQ M9(Oxidation); 1170.576 2.01 Jurkat protein Nup155 naproxen 4 ELQR. ] M19(Oxidation) Calcium-binding [K].sGNGEVTFE photo- 075746 S1(CW_Nap_SiC0N3) mitochondrial carrier 2 866.9075 2.46 Jurkat NVKJE] naproxen 4 protein Aralarl [RJ.rDLDPNEVW photo- Serine/threonine- 094804 E!VGELGDGAFG R1(CW_lndo_SiC2N3) 1004.136 3.44 indomethacin protein kinase 0 K.[V] [K .FKSSLEV i CSECPTVFVDAE L10(CW_Nap_SiC2N3); Protein furry homolog- photo- 094915 3 1422.674 3.69 Jurks TL ScGLLETLK [ C27(Carbamidomethyl) naproxen 4 F]

[R].GVALLRPEPL T 17(CW_Cele_SiC0N3); photo- 095870 Protein ABHD16A 3 1129.877 3.48 Jurkat HRGTADtLLNr [V] R21 (CW_Cele_SiC2N3) ceiecoxib 5

M7(Oxidation); o l9(CW_minimalist_Si2N3) [RJ.DDGSTLmEiD 096019 Actin-like protein 6A 2 1055.002 2.58 K562 tag 7 GDKgK.[Q] G14(CW_minimalist_Si2 N3)

[ ] QWeSAYEVI L-lactate photo- P00338 w 2 859.9495 2.94 Jurkat K.[L] - dehydrogenase A chain naproxen 4

[jq QWESAYEVI L-lactate photo- P00338 v S 2 859.9495 2.13 Jurkat K.[L] - dehydrogenase A chain naproxen 4

[R].LKNDQANYS photo- P00813 L16(CW_Cele_SiC2N3) Adenosine deaminase 3 918.7596 6.19 Jurkat L TDDPIIFK [S] ceiecoxib

[RJ.LKNDQANYS photo- P00813 D14(CW_Cele_SiC2N3) Adenosine deaminase 3 918.7596 2.93 Jurkat LNTDdPL FK [S] ceiecoxib 5

[KJ.NDQANYSLN photo- P00813 F16(CW_Ceie_SiC2N3) Adenosine deaminase 2 1257.046 4.17 Jurkat TDDPLIfK.iS] celecoxib 5 [K .NDQA YSL photo- P0081 3 D 12(CW__Cele__SiC2N3) Adenosine deaminase 1257.046 Jurkat TDdPLI FK.[S] ceiecoxib [K]. ISTQADTIgTE Hemoglobin subunit photo- P02008 G9(C Ce!e SiC2N3) 1090.492 2.53 K562 TLER.[L] zeta ceiecoxib [K]. ISTGAdTIGTE Hemoglobin subunit photo- P02008 D6(CW_Cele__SiC2N3) 2 1090.492 1.88 (562 TLER.[L] zeia ceiecoxib [ .ISTQADTIGtE Hemoglobin subunit T 10(CW__Cele__SiC2N3) 2 1090.493 2.62 K562 TLER.[L] zeia ceiecoxib [K]. ISTQADTIGTe Hemoglobin subunit photo- P02008 E (CW__Nap__SiC2N3) 2 1045.01 9 3.37 K562 TLER.[L] zeta naproxen [K]. !STQADTIGT Hemoglobin subunit photo- P02008 E 14(C Nap SiC2N3) 2 1045.01 9 2.23 (562 ETLeR. [L] zeta naproxen [ .ISTQADTIGTe Hemoglobin subunit photo- E 1 (CW_ Nap SiC2N3) 2 5.01 9 3.38 K562 TLER.[L] zeta naproxen [K .ISTQADTIGtE Hemoglobin subunit photo- P02008 T 1Q(CW_ Nap__SiC2N3) 1045.01 9 1.47 K562 TLER.[L] zeta naproxen [Rj. KEAEScDcLQ P04350; C6(Carbamidomethyl); GFQLTHsLGGGT photo- P07437; C8(Carbamidorrseihyi); Tubulin beta-4A chain 996.9529 5.57 Jurkat GSGMGTLL!SK.[I celecoxib P68371 S 7(C Cele__SiC2N3) ] [Rj. KeAEScDcLQ P04350; E2(CVV _Cele__SiC2N3); GFQLTHSLGGG photo- P07437; C6(Carbamidomethyl); Tubulin beta-4A chain 3 1328.927 3.38 Jurkat TGSGMGTLLISK. ceiecoxib 5 P68371 C8(Carbamidomethyl) [I] PQ4350; [K]. LtTPTYGDLN photo- PQ7437; HLVSATMSG VTT T2(CW__Nap__SiC2N3) Tubulin beta-4A chain 1035.846 2.38 Jurkat naproxen 4 P68371 CLR. [F] P04350; [K]. LTTPTYGDLN photo- P07437; HLVsATMSG VTT S 4(C Nap SiC2N3) Tubulin beta-4A chain 1553.266 2.64 Jurkat naproxen P68371 CLR. [F] P04350; [K]. LTtPTYGDLN photo- P07437; HLVSATMSG VTT T3(CW Nap__SiC2N3) Tubulin beta-4A chain 777. 1367 3.79 Jurkat naproxen P68371 CLR. [F] [ .V IHDNFGIVE Giyceraldehyde-3- L 12(CW Ceie SiC0N3) photo- P04406 GlmTTVHAiTATQ phosphate 1577.763 3.05 Jurkat M 3(Oxidation) ceiecoxib K .[T dehydrogenase HLA class [Rj.APWIEQEGP histocompatibility photo- P04439 E15(CW_Nap_SiC2N3) 1294.586 2.22 Jurkat EYWDQeTR.fN] antigen, A-3 alpha naproxen chain [R].LPEEWSQWL GGSSWPgYVRP Heat shock protein beta- photo- P04792 G16(CW_Nap_SiC2N3) 1516.425 4.6 LPPAAIESPAVAA 1 naproxen PAYSR.[A] Do!ichy!- diphosphooiigosacchari [K].YI_AILGSVtFL photo- T9(CW_Nap_SiC0N3) de protein 1024.062 2.85 K562 AGNR.[M] naproxen glycosyltransferase subunit 2 [Rj.lsLVLGGDHS photo- P05089 LAIGSISGHAR.[V S2(CW_Nap_SiC2N3) Arginase-1 1257.675 2.54 K562 naproxen

[R].EGNDLYHel\ ATP synthase subunit photo- P06576 E8(CW_Cele_SiC2N3) 1303.581 2.71 K562 ESGV!NLK.[D] beta, mitochondrial ce!ecoxib 5

[R].EGNDLYHeA ATP synthase subunit photo- P06576 E8(CW_Cele_SiC2N3) 1303.581 2.43 K562 ESGViNLKJDl beta, mitochondrial celecoxib 5

[RJ.AIAELGIyPAV nit photo- DPLDSTSR celecoxib

[RJ.AIAELGIYPAV ATP synthase subunit photo- P06576 5(CW_Cele_SiC2N3) I267.097 2.52 DPLdSTSR.[i] beta, mitochondrial ceiecoxib 5

[RJ.alAELGIYPAV ATP synthase subunit photo- P06576 (CW_Cele_SiC2N3) 1267.096 3.32 K562 DPLDSTSR.il] beta, mitochondrial celecoxib 5

photo- 2 1267.096 3.07 K562 P06576 7 CW Cete S N3> ceiecoxib 5 [Rj.AiAELGIYPAV ATP synthase subunit photo- P06576 i2(CW Ceie SiC2N3) 2 1267.097 3.83 Jurkat DPLDSTSR.[I] beta, mitochondrial ceiecoxib 5

[Rj.AIAeLGIYPAV ATP synthase subunit P06576 E4(CW Ceie SiC2N3) 2 1267.097 1.79 Jurkat DPLDSTSR . beta, mitochondrial celecoxib 5

[Rj.AiAELGIYPAV ATP synthase subunit photo- P06576 D15(CW ap SiC2N3) 2 1221 .626 2.62 K562 DPLdSTSR.m beta, mitochondrial naproxen

[Rj.AIAELGIyPAV photo- P06576 Y8(CW Nap SiC2N3) P y b 2 1221 .626 1.43 K562 DPLDSTSR.[lj ~ beta,÷ mitochondrial naproxen 4 [Kj.mSVQPTVSLg 1(Oxidation); photo- P06748 GFEITPPWLRJL Nucleophosmin 2 1394.688 2.1 K562 G 10(CW_Cele_SiC2N3) ceiecoxib ] [K].MSVQPTVSL photo- P06748 GGFelTPPVVLR.f E 13(CW_Cele_SiC2N3) Nucleophosmin 2 1386.689 2.43 K562 ceiecoxib 5 L] [Kj.MSVQPTVSL photo- P06748 GGFe!TPPVVLR.[ E 13(CW_Cele_SiC2N3) Nucleophosmin 2 1386.689 2.12 K562 celecoxib 5 L] [Kj.MSVQPTVSL photo- P06748 GGFeiTPPVVLR.[ E 13(CW Cele_SiC2N3) Nucleophosmin 1386.695 2.39 celecoxib 5 L] [Kj.MSVQPTVSL photo- P06748 GGFelTPPVVLR.[ E 13(CW_Cele_SiC2N3) Nucleophosmin 2 1386.689 2.42 Jurkat celecoxib 5 L] [Kj.MSVQPTVSL photo- P06748 GGFelTPPVVLR.[ E 13(CW_Cele_SiC2N3) Nucleophosmin 2 1386.689 2.5 Ju celecoxib 5 L] [Kj.MSVQPTVSLg photo- P06748 GFEITPPWLR.fL G10(CW_Cele_SiC2N3) Nucleophosmin 2 1386.693 1.97 Jurkat celecoxib 5 ] [Kj.MSVQPTVSL photo- P06748 GGFelTPPVVLR.[ E13(CWJndo_SiC2N3) Nucleophosmin 141 1.224 1.82 K562 indomethacin L] [KJ.VdNDENEHQ photo- D2(CW_Nap_SiC2N3) Nudeophosmin 1 .974 2.19 K562 LSLR.jT] naproxen 4 [K].vDNDENEHQ photo- P06748 V1(CW_Nap_SiC2N3) Nudeophosmin 674.9855 2.18 K562 LSLR.[T] naproxen 4 [K].VDNDENeHQ photo- P06748 E7(CW_Nap_SiC2N3) Nudeophosmin 101 1.974 2.62 K562 LSLR.pT] naproxen 4 [ . DNDENEHQ photo- P06748 V1(CW_Nap_SiC2N3) Nudeophosmin 1 11.974 1.77 K562 LSLR.[T] naproxen 4 [K].vDNDENEHQ photo- P06748 V1(CW_Nap_SiC2N3) Nudeophosmin 674.9851 3.34 K562 LSLR.[T] naproxen 4 [K].mSVQPTVSL 1(Oxidation); photo- GGFelTPPVVLR.[ Nudeophosmin 1349.215 2.94 K562 E13(CW_Nap_SiC2N3) naproxen 4 L] [KJ.mSVQPTVSL M 1(Oxidation); photo- P06748 GGFe!TPPVVLR.[ Nudeophosmin 1349.215 1.35 K562 E13(CW_Nap_SiC2N3) naproxen 4 L] [KJ.MSVQPTVSL photo- P06748 GGFe!TPPVVLR.[ E 13(CW_Nap_SiC2N3) Nudeophosmin 1341 .215 2.8 K562 naproxen 4 L] [KJ.MSVQPTVSL photo- P06748 GGFe!TPPVVLR.[ E 13(CW_Nap_SiC2N3) Nudeophosmin 1341 .215 2.73 K562 naproxen 4 L J [KJ.MSVQPTVSL photo- P06748 GGFe!TPPVVLR.[ E 3(CW_Nap SiC2N3) Nudeophosmin 1341 .218 3.08 Jurkai naproxen 4 L] [KJ.MSVQPTVSL photo- P06748 GGFelTPPVVLR.[ E13(CW_Nap_SiC2N3) Nudeophosmin 1341 .218 3.04 Jurkat naproxen 4 L] [KJ.MSVQPtVSLG photo- P06748 GFEITPPWLRJL T6(CW_Nap_SiC2N3) Nudeophosmin 894.4792 2.03 Jurkat naproxen 4

[KJ.AIGAVPLIQgE G10(CW_Cele_SiC2N3); photo- P07339 Cathepsin D 1267.589 2.69 Jurkat YM!PcEK.[V] C16(Carbamidomethyl) celecoxib 5

[KJ.AIGAVPLiQG !8(CW_Cele__SiC2N3); photo- P07339 Cathepsin D 1267.589 2.01 Jurkat EYMIPcEK.[VJ C 16(Carbamidomethyl) celecoxib G10(CWJndo_SiC2N3): photo- [Kj.AiGAVPLiQgE P07339 M13(Oxidaiion); Caibepsin D 1300.121 2.64 K562 indomethacin YmiPcEK.[V] C 6(Carbamidomethyi) 6 Y12(CW_!ndo_SiC2N3); photo- [Kj.AIGAVPLIQG P07339 M13(Oxidation); Catbepsin D 1300.121 1.56 K562 indomethacin EymiPcEK.[V] C16(Carbamidomethyl) 6 phoio- [Kj.AIGAVpLIQGE P6(CWJndo SiC2iM3); P07339 „ Cathepsin D 1292.127 1.61 K562 indomethacin YMIPcEK.[Vj C16(Carbamidomethyl)

E (C __Nap SiC2N3); [Kj.AIGAVPLIQGe „ photo- P07339 M13(Oxidation); Catbepsin D 1230.1 15 2.56 K562 Ym PeEK.[ ] naproxen 4 C 16(Carbamidomethyl) Y 12(CV Nap SiC2N3); [Kj.AIGAVPLIQG photo- P07339 M13{Oxidation); Cathepsin D 1230.1 14 2.99 Jurkat EymlPcEK.[V] naproxen 4 C 6(Carbamidomethyl) Q9(CW_Nap SiC2N3); [Kj.AIGAVPLIqGE „ photo- P07339 M13(Qxidation); Catbepsin D 1230.1 14 1.92 Jurkat YmlPcEK.[V] naproxen 4 C 6(Carbamidomeihyl)

[Kj.AIGAVPLIQG Y12(CW_Nap_SiC2N3); photo- P07339 Catbepsin D 1222.1 19 1.76 Jurkat EyMIPcEK.[Vj C 6(Carbamidomethyl) naproxen 4

[Rj.ALTVPeLTQQ photo- P07437 E6(CW_Ce!e__SiC2N3) Tubulin beta chain 1103.028 1.93 Jurkat VFDAK.[Nj ce ec xib 5 [Rj.AILVDLePGT E7(CW_Ceie_SiC2N3); photo- P07437 Tubulin beta chain 2 1088.995 3.04 Jurk mDSVR.[S] 1(Oxidation) ceiecoxib photo- [Rj.ALTVPeLTQQ P07437 E6(CWJndo SiC2N3) Tubulin beta chain 2 1127.564 2.44 Jurkat indometbacin VFDAK.FNj 6 photo- P07437 vFDAK Q v 4 ( - S 2 N 3 ) Tubulin beta chain 1127.564 2.35 Jurkat indometbacin 6 photo- P07437 K15(CW indo SiC2N3) Tubulin beta chain 1127.564 2.94 Jurkat indomethacin photo- [R].ALTvPELTQQ P07437 V4(CW_indo_SiC2N3) Tubulin beta chain 1127.564 1.81 Jurkat indomethacin VFDA K [N] 6 photo- [Rj.ALTVPELTQQ P07437 D13(CW_lndo_SiC2N3) Tubulin beta chain 1127.564 2.65 Jurkat indomethacin VFdAK.[N] 6 [KJ.TFVNITPAeV photo- P07737 E9(CW_Cele_SiC2N3) Profilin-1 1095.052 2.79 Ju GVLVGK.fD] ceiecoxib 5 [KJ.TFVNITPaEV photo- P07737 A8(CW_Cele_SiC2N3) Profilin-1 1095.052 1.62 Jurkat GVLVGK.[D] ceiecoxib [K].SLc!PFKPLCE Bifunctional C3(Carbamidomethyl); photo- P07814 LQPGAKCVCGk.[ glutamate/proline- 1422.21 1 2.54 K562 K22(CW_Nap_SiC0N3) naproxen 4 N] tRNA iigase Bifunctional [K].iNEAVECLLSL photo- P07814 1 (CW_Nap_SiC2N3) glutamate/proline- 1267.18 2.69 K562 KAQYKEK.jTJ naproxen 4 tRNA iigase Bifunctional [Kj.iNEAVECLLSL photo- P07814 1 (CW_Nap_SiC2N3) g!utamate/proline- 1267.182 2.71 K562 KAGYKEK.jT] naproxen 4 tRNA iigase [Kj.LGLglDEDEV AAEEPNAAVPDE . Heat shock protein HSP photo- P08238 G4(CW_Nap_SiC2N3)« « 1329.617 4.49 K562 IPPLEGDEDASR g o b naproxen 4

[Klj.LGLGIdEDEV AAEEPNAAVPDE Heat shock protein HSP photo- P08238 D6(CW_Nap_SiC2N3) 1993.927 3.09 K562 IPPLEGDEDASR. 90-beta naproxen 4

[RJ.AIVAIEnPADV 40S ribosomal protein photo- P08865 N7(CW_Cele_SiC2N3) 2 1143.555 3.84 K562 SVISSR.[N] SA celecoxib S [RJ.AIVAIeNPADV 40S r bosoma protein photo- P08865 E6(CW_Cele_SiC2N3) 2 1143.555 2.62 K562 SVISSRJNl SA ceiecoxib 5 C3(Carbamidomethyi); , . . K6(CW minimalist Si2N3 ., . . [Kj.ENcNGkmATL ~ .„ . ~ . 39S bosoma protein P09001 1047.521 2.64 K562 g SVGgK T i i , ' L3, mitochondrial G14(CW__mmimahst__Si2 N3) [KJ.DqQEAALVD Glutathione S ~ photo- P0921 1 MVNDGVEDLR.[ Q2(CW_Cele _SiC2N3) 2 1331 .578 3.2 K562 transferase P ceiecoxib C] [KJ.DQQeAALVD Glutathione S- photo- P0921 1 MVNDGVEDLR.[ E4(CW_Cele _SiC2N3) 2 1331 .578 2.47 K562 transferase P celecoxib C] [KJ.AFLASPeYVN Glutathione S- photo- P0921 1 E7(CW_Nap__SiC2N3) 2 1179.605 3.12 K562 LPINGNGK.fQ] transferase P naproxen [KJ.AFLASpEYVN Glutathione S- photo- P0921 1 P6(CW_Nap_ SiC2N3) 2 1179.605 2.14 K562 LPINGNGK.[Q] transferase P naproxen [KJ.AFLASPEyVN Glutathione S- photo- P0921 Y8(C Nap _SiC2N3) 2 1179.604 3.46 Jurkat LPINGNGK.[Q] transferase P naproxen [KJ.AFLASpEYVN Glutathione S- photo- P0921 1 P6(CW_Nap__SiC2N3) 2 1179.604 2.29 Jurkat LPiNGNGK.[Q] transferase P naproxen [R].gDEELDSL!K.[ photo- P0C0S5 G1(CW_Cele _SiC2N3) Histone H2A.Z 2 832.3609 2.7 K562 A] celecoxib [Rj.GDeELDSLIK. photo- P0C0S5 E3(CW_Cele. SiC2N3) Histone H2A.Z 2 832.3609 1.42 K562 [A] celecoxib [Rj.VGATAAVYS photo- PQC0S5 AAILEYLTAeVLE E19(CW_Cele _SiC0N3) Histone H2A.Z 4 860.4278 5.16 Jurkat celecoxib LAGNASK.[D] [Rj.VGATAAVYS photo- PQC0S5 AAILEYLTAeVLE E19(CW_Cele _SiC0N3) Histone H2A.Z 4 860.4278 4.67 Jurkat ceiecoxib LAGNASK.[D]

[KJ.LDmLVASVG M3(Oxidation); Cystathionine beta- photo- P D 79 2 1151 .608 2.59 K562 TGGTITGIAr.[K] R19(CW_Nap_SiC2N3) synthase-like protein naproxen [K].LeVQATDREE photo- P 1387 E2(CW_Cele SiC2N3) DNA topoisomerase 1 3 659.6251 3.61 Jurkat NK.[Q] „ celecoxib [RJ.GIWHNDNKT photo- P12277 FLVwVNEEDHLR W13(CW_Nap )_SiC0N3) Creatine kinase B-type 2 1537.752 1.77 K562 naproxen [V] [RJ.NLeALALDLM X-ray repair cross- P12956 EPEQAVDLTLPK. E3(CW Ceie _SiC2N3) complementing protein 2 1484.731 2.56 K562 " ceiecoxib V 6 [RJ.NIEALALDLM X-ray repair cross- photo- P12956 EPEQAVDLTLPK. L2(CW_Cele__SiC2N3) complementing protein 2 1484.713 2.73 K562 celecoxib 5 [V] 6 [R] nLEALA LDLM X-ray repair cross- P12956 EPEQAVDLTLPK. N1(CW_Cele_SiC2N3) complementing protein 2 1484.725 2.69 Jurkat celecoxib 5 [V] 6 [Rj.nLEALALDLM X-ray repair cross- photo- P12956 EPEQAVDLTLPK. N1(CW miniGL_Ss2N3) complementing protein 2 1417.225 3.53 Jurkat g!utarimide 8 [V] 6 [Rj.nLEALALDLM X-ray repair cross- photo- P12956 EPEQAVDLTLPK. N1(CW_miniGL_Si2N3) complementing protein 1417.223 3.4 Jurkat g!utarimide 8 [V] 6 [Rj.NIEALALDLm X-ray repair cross- L2(CW_Nap__SiC2N3); photo- P12956 EPEQAVDLTLPK. complementing protein 2 1447.247 3.4 K562 MlO(Oxidaiion) naproxen 4 [V] 6 [Rj.NIEALALDLm X-ray repair cross- L2(CVV_Nap_ SiC2N3); photo- P12956 EPEQAVDLTLPK. complementing protein .247 1.81 K562 MIQ(Oxidation) naproxen [V] 6 [Rj.nLEALALDLM X-ray repair cross- photo- P12956 EPEQAVDLTLPK. N1(CW__Nap SiC2N3) complementing protein 1439.245 3.73 K562 naproxen [V] 6 [Rj.nLEALALDLM X-ray repair cross- photo- P12956 EPEQAVDLTLPK. N1(CWJsSap SiC0N3) complementing protein 1438.24 2.58 K562 naproxen [V] 6 [Rj.NLeALALDLM X-ray repair cross- photo- P12956 EPEQAVDLTLPK. E3(C Nap SiC2 3) complementing proiein 1439.248 1.43 K562 naproxen [V] 6 [Rj.NLEALALDLm X-ray repair cross- photo- P12956 EPEQAVDLTLPK. M1 (C Nap SiC2 3) complementing proiein 1439.251 1.66 Jurkat naproxen [V] 6 [RJ.NIEALALDLM X-ray repair cross- photo- P12956 EPEQAVDLTLPK. L2(CW__Nap__SiC2N3) complementing protein 1439.241 3.04 Jurkat naproxen [V] 6 [Rj.NIEALALDLm X-ray repair cross- L2(CWjTiinimalist_Si2N3 P12956 EPEQAVDLTLPK. complementing protein 2 1348.21 1 3.81 Jurkat taq 7 } ; MIQ(Oxidation) V] [Rj.GHVFEeSQV photo- P13639 E6(CW_Nap_SiC2N3) Elongation factor 2 2 1208.598 2.88 K562 AGTPMFVVK.fA] naproxen 4

[RJ.GHVFEESQV photo- P13639 G 11(CW_Nap_SiC2N3) Elongation factor 2 2 1208.598 1.34 K562 AgTP FVVK. ] naproxen 4

[Rj.GHVFEeSQV photo- P13639 E6(CW_Nap_SiC2N3) Elongation factor 2 1208.595 3.45 K562 AGTPMFVVK.[A] naproxen 4

[RJ.QFVTATDW photo- P13796 RGNPKLNLAFIA F24(CW_lndo_SiC2N3) Plastin-2 1171 .619 1.73 K562 indomethacin NLfNR.iY]

P14625; [Rj.ELiSNASDAL 3(CW_lndo_SiC2N3) Endoplasmin 2 935.4396 2.14 Jurkat indomethacin P08238 DK.[I]

P14625; [Rj.eLISNASDAL photo- E1(CW_Nap_SiC2N3) Endoplasmin 2 865.4326 2.42 K562 P08238 DK.[I] naproxen M7(Oxidation); [Rj.QDSLESmKF photo- P15924 G10(CW_Nap_SiC2N3); Desmoplaksn 2 1216.051 1.34 K562 gDSNTVmR.[F] naproxen M16(Oxidation) P16402; [KJ.ALAAAGYDvE photo- P1Q412; V9(CW_Cele_SiC2N3) Histone H1.3 2 826.8662 2.43 K562 K.[N] celecoxib P16403 P16402; [Kj.ALAAAGYDVe photo- P10412; E10(CW_Cele_SiC2N3) Histone H1.3 2 826.8662 1.37 K562 K.[N] celecoxib 5 P16403 P16402; [KJ.ASGPPVsELI photo- S7(CW_Nap_SiC2N3) Histone H1.3 2 826.9437 1.78 Jurkat P16403 TK.[A] naproxen 4 [K].dTEEPLPVK.[ photo- P18583 D1(CW_Nap_SiC2N3) Protein SON 2 741 .3789 2 6 K562 E] naproxen 4 Voltage-dependent [RJ.WTEYGLTFtE photo- P21796 T9(CW_Cele_SiC2N3) anion-selective chann? 2 960.4106 2.84 Jurkat K.[W] celecoxib 5 protein 1 Heierogeneous nuclear [Rj.QEmQEVQSS phoio- P22626 3 (eW Ceie SiC2N3) ribonudeoproteins 883.8578 1.77 K562 R.[Sj celecoxib 5 A2/B1

[Kj.GkGFGFIKLE Splicing factor, proiine- photo- P23246 K2(CW eie SiC0N3) 539 2.38 K562 SR.[A] and glutamine-rich ceiecoxib 5 photo- P3 46 [R].LeETVQAK [~] E2(CW Cele SiC 3) Coronin-1A 731 .8301 2.39 Jurkat celecoxib 5 photo- [Rj.ATeNDIANFF Heterogeneous nuclear P31942 E3(CWJndo SiC2N3) 1257.103 2.34 Jur indomethacin SPLNPIR.[V] ribonucleoprotein H3

photo [RJ.ATENDIANFF Heterogeneous nuclear P31942 i6(CWJndo_SiC2N3) ' s 257. 103 1.57 Jurkat indomethacin SPLNPIR.jV] ribonucleoprotein H3 6 photo- P31943; [RKj.ATeNDIYNF Heterogeneous nuclear E3(CWJndo SiC2N3) 1296.104 2.42 Jurkat indomethacin P52597 FSPLNPVR.fV] ribonucleoprotein H 6 [Kj.yEIAVETEMK Y1(CW_minimaiist_Si2N3 Replication factor C P35251 2 970.994 2.99 K562 tag 7 KESK.[L] ) subunit 1 [Kj.iAQLeEQLDN photo- P35579 E5(CW_ Ce!e SiC2N3) Myosin-9 2 1038.463 2.92 Jurkat ETK.[E] ceiecoxib 5 [KJ.IAQIEEQLDN photo- P35579 L4(CW_Cele_SiC2N3) Myosin-9 1038.463 1.55 Jurkat ETK.[E] ceiecoxib 5 [KJ.LQVELDnVTG photo- P35579 N7(CW_Cele_SiC2N3) Myosin-9 1246.087 1.93 Jurkat LLSQSDSKISl ceiecoxib 5

P35658 [R]-STAPASLsR.[ S8(CW_minirnalist_Si2N3 Nuclear pore complex 573.3164 1.66 K562 tag 7 S ) protein Nup214

, , T6(CW Nap SiC0N3i; _ . . . , photo- P369 S 3(C Nap SiCONS); ™ e nudeo ,de 1546.257 1.64 Jurkat DLssWR.[E] s (C Nap SiC0N3 b n d P - naproxen 4 [Klj.GSADPLNsAF Superkii!er viralicidic photo- P42285 HLTYNMVLNLLR. S8(CW_Nap_SiC2N3) 1450.734 2.64 K562 activity 2-!ike 2 naproxen 4 [V] Voltage-dependent [R].NNFAVGyR.[T photo- P45880 Y7(CW_Cele_SiC2N3) anion-selective channel 3149 2.6 K562 celecoxib 5 protein 2 Phosphatidylinosiiol [ j.N TGGGEGIE P48739 E2(CW_Cele_SiC2N3) transfer protein beta 924.4091 2.37 Jurkat VLK.[N] ceiecoxib 5 isoform Phosphatidylinositol [KJ.nETGGGEGIE photo- P48739 N1(CW_Cele_SiC2N3) iransfer protein beta 1 1.61 Jurkat VLK.[N] ceiecoxib isoform [KJ.rPEAAQLLED R1(CW_minimalist_Si2N3 Cysteine-tRNA ligase, P49589 VQAALKPFSVK [ 642.3577 3.25 K562 tag 7 ) cytoplasmic L] [K].YSHVDLWM Serine-tRNA ligase, photo- P49591 VDGFEGEKGAV S24(CW_Nap_SiC0N3) 1025.172 2 1 K562 cytoplasmic naproxen 4 VAGsR [G] [K].YSHVDLWM Serine-tRNA ligase, phoio- P49591 VDGFEGEKGAV A22(CW_Nap_SiC0N3) 1025.171 1.84 Jurkat cytoplasmic naproxen 4 VaGSR.[G] [RJ.FGPYYTePV! Proteasome subunit photo- P49720 E7(CW_Nap_SiC2N3) 1111.057 3.4 Jurkat AGLDPK [T] beta type-3 naproxen 4 [RJ.FGPYyTEPVI Proteasome subunit photo- P49720 Y5(CW_Nap_SiC2N3) 2 1111.057 1.58 Jurkat AGLDPK.[T] beta fype-3 naproxen 4 [Rj.FGPYYTePVI Proteasome subunit photo- P49720 E7(CW_Nap_SiC2N3) 2 1111.058 3.34 Jurkat AGLDPK.[T] beta type-3 naproxen 4 Very long-chain specific [K].YLPKLASgET acyl-CoA VAAFCLTEPSSG G8(CW_Cele_SiC2N3) 1162.887 3.44 K562 dehydrogenase, ceiecoxib 5 SDAASIR.[T] mitochondrial [Rj.AFADAmEvlP photo- M6(Oxidation); T-comp!ex protein 1 P50991 STLAENAGLNPI 1214.26 2.81 K562 indomethacin V8(CW !ndo SIC2N3) subunit delta STVTELR.[N] [Rj.AFADAMEViP T-compiex protein 1 photo- P50991 STLAENAGLNPI l9(CW_Nap_SiC2N3) 2 1742.878 2.64 K562 subunit delta naproxen 4 STVTELR.[N] [RJ.AFADAMEvlP T-complex protein 1 photo- P50991 STLAENAGLNPI V8(CW_Nap_SiC2N3) 3 1162.258 3.14 K562 subunit delta naproxen 4 STVTELR.[N] [RJ.AFADAMEvlP T-compiex protein 1 photo- STLAENAGLNPI V8(CW_Nap_SiC2N3) 2 1742.878 2.98 K562 subunit delta naproxen 4 STVTELR.[N] [RJ.AFADAMEVIP T-compiex protein 1 photo- P50991 sTLAENAGLNPIS S 11(CW_Nap_SiC2N3) 1162.255 3.43 Jurkat subunit delta naproxen 4 TVTELR.[N] [RJ.AFADAMEVIP T-compiex protein 1 photo- P50991 STLAEnAGLNPIS N16(CW_Nap_SiC2N3) 3 1162.255 3.22 Jurk subunit delta naproxen 4 TVTELR.[Nj [Rj.AEEY EFLTPV Rho GDP-dissociation photo- P52565 E 1 1(CW_Cele_SiC2N3) 4.05 Jurkat eEAPK.fG] inhibitor 1 ceiecoxib 5

[Rj.AEEYEFLTPv Rho GDP-dissociation photo- P52565 V 10(CW_Cele_SiC2N3) 2 1149.001 1.76 Jurkat EEAPK.[G] inhibitor 1 celecoxib 5

j.MAEQEPTAEQL Y27(CW_minimalist_Si2N Rho GDP-dissociation P52565 3 1317.956 3.5£ tag 7 AQIAAENEEDEH 3) inhibitor 1 SVNyKPPAQK.[S] [Kj.ATFmVGSYG M4(Oxidation); Rho GDP-dissociation photo- P52566 PRPEEYEFLTPV 1169.19 5.55 Jurkat E22(CW_Cele_SiC2N3) inhibitor 2 celecoxib 5 eEAPK.[G] [KJ.ATFMVGSYG Rho GDP-dissociation photo- P52566 PRPEEYEFLTPV A24(CW_Cele_SiC2N3) 3 1163.858 3.71 Jurkat inhibitor 2 celecoxib 5 EEaPK.[G] [Kj.ATFmVGSYG M4(Oxidation); Rho GDP-dissociation photo- P52566 PRPEEYEFLTPV 3 1138.873 4.57 Jurkat V21 (CW_Nap_SiC2N3) inhibitor 2 naproxen 4 EEAPK.[GJ [KJ.ATFmVGSYG M4(Oxidation); Rho GDP-dissociation photo- P52566 PRPEEYEFLTpV 3 1138.874 3.98 Jurkat P20(CW_Nap_SiC2N3) inhibitor 2 naproxen 4 EEAPK.[G] [K].ATFMVGSYG Rho GDP-dissociation photo- P52566 PRPEEYEFLTpV P20(CW Nap SiC2N3) 3 1133.541 4.46 Jurkat „ „ naproxen 4 EEAPK.[G]

P55209; [Kl.FYEEVHDLeR NLfdeosome assembly E9(CW Ceie SiC2N3) 941 .3913 3.42 Jurkat Q99733 protein 1-like 1 ceiecoxib 5

P55209; [KJ.FYEEVHDLeR Nucieosome assembly photo- E9{CVV_Nap_SiC2N3) 2 895.9163 3.41 K562 Q99733 protein 1-like 1 naproxen 4

P55209; [KJ.FYEEvHDLER. Nucieosome assembly photo- V5(CW_ Nap_SiC2N3) 2 895.9163 2.27 K562 Q99733 protein 1-like 1 naproxen 4

P55209; [Kj.FYEEVHDLeR Nucieosome assembly photo- E9(CW_ Nap_SiC2N3) 895.9176 2.75 K562 Q99733 protein 1-like 1 naproxen 4 Ribosoma! R A photo- P56182 [R].RILEGR.[R] L2(CW_Nap__SiCQN3) processing protein 1 598.3324 1.36 (562 naproxen 4 homo!og A [RJ.VAPeEHPVLL photo- P60709 E4(CW_Ceie_SiC2N3) Actin, cytoplasmic 1 3 833.7452 3.49 K562 TEAPLNPK.fA] ceiecoxib 5 [R].VAPEeHPVLL photo- P60709 E5(CW Ce!e SiC2N3) Actin, cytoplasmic 1 3 833.7452 3.41 (562 TEAPLNPK.[A] „ „ celecoxib 5 [Rj.VAPeEHPVLL photo- P607Q9 E4(CW_Cele_SiC2N3) Actin, cytoplasmic 1 2 1250.1 11 2.72 K562 TEAPLNPK.[A] ceiecoxib [RJ.VAPEEnPVLL photo- P60709 H6(CW_Cele_SiC2N3) Actin, cytoplasmic 1 2 1250.1 11 2.44 K562 TEAPLNPK.fA] ceiecoxib 5 [RJ.VAPEEHPVLL photo- P60709 E12(CW_Ceie SiC2N3) Actin, cytoplasmic 1 2 1250.1 12 3.29 (562 TeAPLNPK.[A] „ celecoxib 5 [RJ.VAPEEHPVLL phoio- P60709 E12(CW Cele SiC2N3) Actin, cytoplasmic 1 2 1250.1 12 1.69 K562 TeAPLNPK.[A] „ ceiecoxib 5 [RJ.VAPEEHPVLL photo- P60709 T 11(CW__Ce!e__SiC2N3) Actin, cytoplasmic 1 1250.1 13 2.75 K562 tEAPLNPK.IA] celecoxib 5 FRl VAPFPHPVI ! photo- P607Q9 ™ " „ E5(CW_Cele_SiC2N3) Actin, cytoplasmic 1 833.7452 1.9 K562 i bArLNrr\. [Aj ceiecoxib 5 P photo- P60709 S A2(CW Cele SiC2N3) Actin, cytoplasmic 1 1250.1 14 3.05 K562 TEAPLNPK.[A]S v _ _ ceiecoxib 5 [RJ.TTGIVmDSG photo- P607Q9 DGVTHTVPIYEG A c n - cytoplasmic 1 1248.924 4.91 K562 yALPHAILR.[L] ceiecoxib [RJ.TTGlVmDSGd photo- P607Q9 GVTHTyPiYEGY Actin, cytoplasmic 1 1248.924 2.37 K562 ceiecoxib 5 ALPHM !LR.[Lj r p VAPFPHPV ! photo- P60709 , r E5(CW Cele SiC2N3) Actin, cytoplasmic 1 833.7466 1.63 K562 TEAPLNPK.[A]™ celecoxib 5 [RJ.TTGIVMDSG photo- P607Q9 DGVTHTVPIYeG E20(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1243.591 4.91 K562 ceiecoxib 5 YALPHAILR.[L] [RJ.TTGIvMDSGD photo- P607Q9 GVTHTVPIYEGY V5(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1243.591 2.21 K562 ceiecoxib ALPHAILR.[L] photo- P60709 CW Cele SiC2N3) Actin, cytoplasmic 1 1250.1 11 3.65 Jurkai _ _ celecoxib 5 photo- P607Q9 CW Cele SiC2N3) Actin, cytoplasmic 1 1250.1 11 1.78 Jurkat - ceiecoxib 5 photo- P60709 E4(CW Cele SiC2N3) Actin, cytoplasmic 1 833.7452 3.06 Jurkat TEAPLNPK.[A]S _ _ ceiecoxib 5 [RJ.TTGIVMDSG photo- P607Q9 DGVTHTVPIYeG E20(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1243.605 3.82 Jurkat ceiecoxib YALPHAILR.fL] [RJ.TTGIVMDSG photo- P607Q9 DGVTHTVPIYEG V16(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1243.605 2.78 Jurkat ceiecoxib 5 YALPHAILR [L] [RJ.TTGIVMDSG photo- P60709 DGVTHTVPiyEG Y19(CW_Cele_SiC2N3) Actin, cytoplasmic 1 932.9508 2.63 Jurkat celecoxib 5 YALPHAILR.[L] [RJ.TTGIVMDSG phoio- P60709 DGVTHTVPIYeG E20(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1243.591 4.78 Jurkai celecoxib 5 YALPHAILR.[LJ K FY P photo- P607Q9 ' E5(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1031 .433 2.6/ Jurkat V .K.[ j ceiecoxib photo- P60709 S E5(CW_Ceie__SiC2N3) Actin, cytoplasmic 1 833.7509 3.98 Jurkat TEAPLNPK.jA] ceiecoxib 5 photo- [R].VAPEEhPVLL H6(CW_lndo_SiC2N3) Actin, cytoplasmic 1 850.1015 3.1 Jurkat indomethacin TEAPLNPK.[A] 6 [Rl.TTGIVmdSGD photo- P60709 GVTHTVPIYEGY . Actin, cytoplasmic 1 1265.28 1.74 Jurkat indomethacin D7(CW_lndo_SiC2N3 ) ALrHAI. , , , L, .[Lj 6 photo- P607Q9 T 11(CW Indo SiC2N3) Actin, cytoplasmic 1 1274.652 2.94 Jurkat indomethacin bAPL K 6 photo- [R].VAPEEHPVLI L10(CW_lndo_SiC2N3) Actin, cytoplasmic 1 850.1026 1.9 Jurkat indomethacin TEAPLNPK.jA] 6 [Rl.TTGIVmdSGD photo- M6(Oxidation); GVTHTVPIYEGY Actin, cytoplasmic 1 949.2144 3.62 Jurkat indomethacin D7(CW_lndo_SiC2N3) ALPHAILR.[L] 6 [KJ.DIYANTVLSG photo- L2(CW_lndo_SiC2N3); GTTmYPGIADR.f Actin, cytoplasmic 1 1413.147 3.41 Jurkat indomethacin 4(Oxida ion) M] 6 [K].dLYANTVLSG photo- D1(CW_lndo_SiC2N3); GTTmYPGIADR.f Actin, cytoplasmic 1 1413.147 3.69 Jurkat indomethacin M14(Oxidation) M] 6 [Rj.VAPEeHPVLL photo- E5(CW_Nap_SiC2N3) Actin, cytoplasmic 1 803.4304 2.7 K562 TEAPLNPK.jA] naproxen 4 [Rj.VAPEeHPVLL photo- E5(CW_Nap_SiC2N3) Actin, cytoplasmic 1 803.429 3.4 Jurkat TEAPLNPK.jA] naproxen 4 [Rj.VAPEeHPVLL photo- E5(CW_Nap_SiC2N3) Actin, cytoplasmic 1 803.429 3.27 Jurkat TEAPLNPK.jA] naproxen 4 [R].TTGIVMDSG photo- DGVTHTVPIYeG E20(CW_Nap_SiC2N3) Actin, cytoplasmic 1 1213.277 3.92 Jurkat naproxen 4 YALPHAILRJLl [R].TTGIVMDSG photo- P60709 DGVThTVPIYEG H14(CW_Nap_SiC2N3) Actin, cytoplasmic 1 3 1213.277 2.4 Jurkat naproxen 4 YALPHAILR.[LJ P60709; [KJ.SYELPDGQVI photo- R16(CW_Cele_SiC2N3) Actin, cytoplasmic 1 2 1168.525 3.67 K562 P68032 TIGNErJFl ceiecoxib P60709; [KJ.SYELPDGQVI E15(CW_Cele_SiC2N3) Actin, cytoplasmic 1 2 1168.525 2.39 K562 P68032 T IGNeR [FJ celecoxib 5 P6Q709; [KJ.SYELPDGQVI photo- R16(CW_Cele_SiC2N3) Actin, cytoplasmic 1 2 1168.529 3.28 K562 P68032 TIGNEr.fFJ ceiecoxib 5 P60709; [KJ.SYELPDGQVI photo- E15(CW_Cele_SiC2N3) Actin, cytoplasmic 1 2 1168.529 2.82 K562 P68032 TIGNeR.fFJ ceiecoxib P6Q709; [KJ.elTALAPSTM photo- E1(CW_Cele_SiC2N3) Actin, cytoplasmic 1 2 853.8927 2.03 Jurkat P68032 K.[l] celecoxib 5 photo- P60709; [KJ.SYELPDGQVI G13(CW_lndo_SiC2N3) Actin, cytoplasmic 1 1193.063 3.03 K562 indomethacin P68032 TlgNER.[FJ 6 photo- P60709; [KJ.SYELPDGQVI E15(CWJndo_SiC2N3) Actin, cytoplasmic 1 1193.063 2.02 K562 indomethacin P68032 TIGNeR.[F] 6 photo- P60709; [KJ.EiTALAPSTM l2(CW_lndo_SiC2N3) Actin, cytoplasmic 1 878.4285 1.62 Jurkat indomethacin P68032 K.[IJ

P6Q709; [KJ.AGFAGdDAP photo- D6(CW_Nap_SiC2N3) Actin, cytoplasmic 1 715.8338 2.95 Ju P68032 R-[A] naproxen 4 P60709; [KJ.AGFAGDdAP photo- D7(CW_Nap_SiC2N3) Actin, cytoplasmic 1 715.8338 2.64 Jurkat P68032 R.[AJ naproxen 4 P60709; [KRJ.SYELPDGQ photo- Q562R1 ; R16(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1168.524 4.01 Jurkat VITIGNEr.[FJ celecoxib 5 P68032 P60709; [KRJ.SYELPDGQ photo- Q562R1 ; E15(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1168.524 2.78 Ju VITIGNeR.[FJ celecoxib 5 P68032 P60709; [KRJ.SyELPDGQ photo- Q562R1 ; Y2(CW_Cele_SiC2N3) Actin, cytoplasmic 1 1168.526 2.53 Jurkat VITIGNER.[F] ceiecoxib 5 P68032 P60709; [KR].sYELPDGQ photo- Q562R1 ; S1(CW Cele SiC2N3) Actin, cytoplasmic 1 1168.526 3.03 Jurkat VITIGNERIF] ceiecoxib 5 P68032 P60709; photo- [KR].SyELPDGQ Q562R1 ; Y2(CW_lndo_SiC2N3) Actin, cytoplasmic 1 1193.067 2.8 Jurkat indomethacin VITIGNERIF] P68032 P60709; [KR].SYeLPDGQ Q562R1 ; E3(CW_lndo_SiC2N3) Actin, cytoplasmic 1 1193.061 2.47 Jurkat indomethacin VITIGNERIF] P68032 P6Q709; photo- [KRJ.SYeLPDGQ Q562R1 ; E3(CW__lndo__SiC2N3) Actin, cytoplasmic 1 1193.061 1.71 Jurkat indomethacin VITIGNER.[F] P68032 P60709; [KRJ.SyELPDGQ photo- Q562R1 ; Y2(CW_Nap_SiC2N3) Actin, cytoplasmic 1 1123.053 2.97 Jurkat VITIGNER.[F] naproxen P68032 [RJ.INNAcFEAWv C5(Carbamidomethyl); Ribose-phosphate photo- P60891 TNTIPQEDKmKH V 11(CW_Nap_SiC0N3); 1148.88 2.89 Jurkat pyrophosphokinase 1 naproxen CSK.[I] M21 (Oxidation) 40S ribosomal protein photo- P62277 [R].LILIeSR.[l] E5(CW_Cele_SiC2N3) 2 694.8479 2.51 (562 S13 celecoxib 40S ribosomal protein P62277 [R].LILIeSR.[l] E5(CW_Cele_SiC2N3) 2 694.8479 1.58 K562 S13 ceiecoxib [Rj.dAVTYTEHAK photo- P62805 D1(CW_Cele_SiC2N3) Histone H4 2 840.3532 2.99 K562 .[R] ceiecoxib [RJ.DaVTYTEHAK photo- P62805 A2(CW_Cele_SiC2N3) Histone H4 2 840.3532 1.68 (562 [R] celecoxib [RJ.DaVTYTEHAK P628Q5 A2(CW_Cele_SiC2N3) Histone H4 3 560.5721 2.02 K562 .[R] ceiecoxib [Rj.DAVTYTeHAK photo- P62805 E7(CW_Cele_SiC2N3) Histone H4 2 840.3528 2.41 K562 .[R] celecoxib [Rj.DAVTYTeHAK photo- P62805 E7(CW_Cele_SiC2N3) Histone H4 2 840.3528 2.04 K562 [R] ceiecoxib [Rj.DAvTYTEHAK P628Q5 V3(CW_Cele_SiC2N3) Histone H4 3 560.5732 1.75 K562 [R] ceiecoxib 5 SO SO s X 3 Χ3 O O o X o x o X o o x o X o X 3 x o x o X x x o X x X a X χ o o o o o o o o o o o O o o o o O o o o o O o o o o Ο ο ο o ϋ χ Φ Φ Φ x Φ φ Q CL ) ) CD a . ) CD a . ) CD CD CD CD CD CD CD CD ϋ ϋ ϋ ϋ ϋ ϋ ϋ ϋ ϋ

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to IO o to IO t t to to t to to t to to t to o O o o O o o o o o o o o o o o o O O O O O O 00 O O 00 O O 00 O O 00 O CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM O CD CD O CD CD O CD CD CO CD CD CO CD CD CO CD OL¬ L Q_ OL¬ CL Q_ a . CL Q_ a . CL Q_ a . CL CL a . CL Κ RiSGLIY EeTR photo- Ρ [ ] . 62 3 5 E9(CW„ Cele_SiC2N3) Hisione H4 3 627.9662 3.36 Jurkat 1 ceiecoxib [Κ] .RiSGLIYEeTR photo- Ρ 62 505 E9(CW Cele_SiC2N3) Histone H4 3 627.9647 3.28 Jurkat [G;! ceiecoxib 5 [Κ] .RiSGLIYEeTR photo- Ρ62 05 E9(CW_ Cele_SiC2N3) Hisione H4 3 627.9657 3.51 Jurkat [G;] celecoxib 5 photo- Ρ [ ] .RiSGLIYEeTR 62 3 5 E9(CW„ Cele_SiC2N3) Hisione H4 3 627.9657 1.93 Jurkat 1 ceiecoxib photo- [R]- ISGLIYEeTR [ Ρ 62ί305 E8(CW_jndo__SiC2N3) Histone H4 2 887.9271 2.38 Jurkat indomethacin G] ISGL YEeTR [ photo- Ρ62 305 [R]- E8(CW__Nap_SiC2N3) Hisione H4 2 817.9197 3.02 K562 G] naproxen 4 ISGLiYEETR .[ photo- Ρ 62 3 5 [R]- I5{CW_ Nap_SiC2N3) Hisione H4 2 817.9197 2.04 K562 G ] naproxen 4 photo- Ρ 62 305 [Κ] .VFLeNVIR [D] E4(CW._Nap_SiC2N3) Histone H4 2 722.3991 2.24 K562 naproxen 4 photo- Ρ62 305 [ ] .VFLeNVIR.[D] E4(CW__Nap_SiC2N3) Histone H4 2 722.3987 2.62 K562 naproxen 4 photo- Ρ 82 305 [Κ] .VFIENVIR.[D] L3(CW__Nap_SiC2N3) Histone H4 2 722.3987 1.35 K562 naproxen 4 Guanine nucleotide- [RJ.DARKAcADAT C6(Carbamidomethyl); binding protein photo- P62873 LSQITNNIDPVGr. 1470.73 2.66 K562 R23(CW_Nap SiC2N3) G(i)/G(S)/G(T) subunit naproxen beta-1 [KJ.SYcAelAHNV C3(Carbamidomethyl); 60S ribosomal protein photo- P62910 1005.919 2.86 K562 SSK.[N] E5(CW_Cele_SiC2N3) ceiecoxib [KJ.TVANmlKgKT M5(Oxidation); S-phase kinase- photo- P63208 1123.532 2.4 Jurkat PEEIR.[K] G8(CW_Cele_SiC0N3) associated protein 1 celecoxib [RJ.VAPEEHPTLI Aciin, alpha cardiac photo- P68032 L10(CW_Cele_SiC2N3) 3 834.4127 1.97 K562 TEAPLNPK.[A] muscle 1 ceiecoxib [K].YPIEHGIITNW Actin, alpha cardiac photo- P68032 K16(CW_Cele_SiC2N3) 3 836.0266 3.62 K562 DDMEk.ni muscle 1 ceiecoxib photo- P68032 N ) Actin alpha cardiac 1274.643 2.32 Jurkat indornethacin muscle 1

o n ,tor „ i E longa fac 1- photo- P K r r C V S D . . . . . 1 191 .515 4.05 K562 ,,-, - C16(Carbamidomethyh; alpha 1 celecoxib 5 S19(CW_Cele_SiC2N3)

[KJ.SGDAAiVdmV D8(CW_Cele_SiC2f Elongation factor 1- photo- P68104 PGKPMcVESFSD M9(Oxidation); 1 186.187 2.61 K562 alpha 1 celecoxib 5 YPPLGR.fF] C16(Carbamidomethyl) [Rj.VETGVLKPG Elongation factor 1- photo- P68104 MVVTFAPVNVTT V1(CW__Ceie__SiC2N3) 1020.849 3.97 K562 alpha 1 celecoxib 5 EVK.[S] [Rj.VETGVLKPG Elongation factor 1- photo- P68104 MVvTFAPVNVTT V12(CW_Cele_SiC2N3) 1020.849 1.77 K562 a p h a 1 celecoxib 5 EVK.[S]

photo- celecoxib 5

[R].VETGVLkPG Elongation factor 1- photo- P681Q4 MVVTFAPVNVTT K7(CW_Cele_SiC2N3) 1020.85 3.63 K562 alpha 1 celecoxib 5 EVK.[S] [Rj.VETGVLKPG Elongation factor 1- photo- P681Q4 MVVTFAPVNVTT V23(CW_Cele_SiC2N3) 1020.851 4.3 K562 alpha 1 ceiecoxib EvK.FS]

[KJ.SGDAAIVDmV S ♦ ♦ photo- P68104 PGKPrncVESfSD E ongaton factor 1- 1 191 .519 4.1 1 Jurkat Ypp . C16(Carbarnidornethyi); alpha 1 celecoxib 5 F20(CW_Cele_SiC2N3) M9(Oxidat!on); [KJ.SGDAAIVDmv V10(CW_Cele_SiC2N3); Elongation factor 1- photo- P68104 PGKPmcVESFSD 3 1191 .519 1.84 Jurkat M15(Oxidation); a pha 1 celecoxib 5 YPPLGR.fF] C 16(Carbamidomeihyi) [R] VeTGVLKPG E2(CW_Cele_SiC2N3); Elongation factor 1- P68104 mWTFAPVNVTT 3 1026.18 3.32 Jurkat MlO(Oxidation) alpha 1 celecoxib 5 EVK.[S] [RJ.VeTGVLKPG E2(CW_Cele_SiC2N3); Elongation factor 1- P681Q4 mWTFAPVNVTT 3 1026.18 2.17 Jurkat MlO(Oxidation) alpha 1 ceiecoxib 5 EVK.[S] [RJ.VETGVLKPG MlO(Oxidaiion); Elongation factor 1- photo- P681Q4 mWTFAPVNVTT 2 1538.769 2.21 Jurkat V23(CW_Cele_SiC2N3) alpha 1 ceiecoxib EvK.[S] [KJ.SGDAAIVDMV C16(Carbamidomethyl); Elongation factor 1- photo- P68104 PGKPMcVeSFSD 3 1180.858 2.48 Jurkat E18(CW_Cele_SiC2N3) alpha 1 celecoxib 5 YPPLGRIF]

[RJ.VETGVLKPG MlO(Oxidaiion); Elongation factor 1- photo- P68104 mWTFAPVNVTT 995.8684 3.89 K562 V23(CW_Nap_SiC2N3) alpha 1 naproxen 4 EvK.[S] [Rj.VeTGVLKPG E2(CW_Nap_SiC2N3); Elongation factor 1- photo- P68104 mWTFAPVNVTT 995.8684 4.94 K562 MlO(Oxidation) alpha 1 naproxen EVK.[SJ [RJ.VETGVLKPG MlO(Oxidaiion); Elongation factor 1- photo- P68104 mvVTFAPVNVTT 995.8684 2.03 K562 V 11(CW_Nap_SiC2 alpha 1 naproxen EVK.[SJ [RJ.VETGVLKPG MlO(Oxidaiion); Elongation factor 1- photo- P68104 mWTFAPVNVTT 1493.299 3.6 K562 K24(CW_Nap_SiC2N3) alpha 1 naproxen EVk.iSJ [RJ.VETGVLKPG Elongation factor 1- photo- P68104 MVVTFAPVNVTT V23(CW_Nap_SiC2N3) 1485.301 3.21 K562 alpha 1 naproxen EvK.[SJ [RJ.FQSSAVmAL QEACeAYLVGLF M7(Oxidation); photo- P68431 Histone H3.1 1345.271 3.72 (562 EDTNLCAIHAK.f E14(CW Ce!e SiC2N3) ceiecoxib [KJ.VGAHaGEYG Hemoglobin subunit photo- P69905 A5(CW_ Ceie_SiC2N3) 692.3029 3.47 Jurkat AEALER.[M] alpha celecoxib 5 [KJ.VGAHAGeYG Hemoglobin subunit photo- P69905 E7(CW_Cele SiC2N3) 2 1037.951 2.92 Jurkat AEALER.[M] alpha ceSecoxib 5 [KJ.VGAHAGEYG Hemoglobin subunit photo- P69905 R15(CW_Cele SiC2N3) 3 692.3027 4.56 Jurkat AEALEr.[M] alpha ceiecoxib 5 [KJ.VGAHAGEYG Hemoglobin subunit photo- P69905 E14{CW_Cele_SiC2N3) 2 1037.951 3.33 Jurkat AEALeR.[M] alpha ceiecoxib 5 [KJ.VGAHAGEYG Hemoglobin subunit photo- P69905 R 15(CW_Ceie__SiC2N3) 3 692.3032 3.88 Jurkat AEALEr.[MJ alpha ceiecoxib 5 [KJ.VGAHAGEYG Hemoglobin subunit photo- P69905 E14(CW_Cele SiC2N3) 3 692.3032 3.23 Jurkat AEALeR.[MJ alpha ceiecoxib 5 [KJ.VGAHAGEYG Hemoglobin subunit photo- P69905 A12(CW Ceie SiC2N3) 1037.95 1.95 Jurkat AEaLER.[M] „ alpha ceiecoxib [R].KQVEELFeR.[ General transcription photo- P78347 E8(CW_Nap_SiC2N3) 2 816.4258 1.65 K562 ] factor li~l naproxen 4 P84243; [R].yRPGTVALR.[ photo- Y1(CW_Cele SiC2N3) Histone H3.3 3 526.59 2.09 Jurkat P68431 E] celecoxib 5 P84243; [RJ.EIAQDFKTdL photo- P68431 ; D9(CW_Ce!e_SiC2N3) Histone H3.3 940.9268 1.78 K562 R.[FJ celecoxib 5 Q7 3 P84243; photo- P68431 ; [K].sT ELLIR [KJ S1(CW Cele SiC2N3) Histone H3.3 2 688.8298 1 64 Jurkat „ ceiecoxib 5 G7 3 [RJ.FKEQLTPSQI Transcription factor A , photo- Q00059 E14(CW_Cele__SiC2N3) 3 775.3702 5.39 Jurks MSLeK.[E] mitochondrial ceiecoxib 5 Phosphatidylinositoi [KJ.NeTGGGEGV photo- Q00169 E2(CVV_Cele_SiC2N3) transfer protein alpha 1283.058 3.1 1 Ju EVLVNEPYEK.[DJ celecoxib 5 isoform Phosphatidylinositoi [KJ.NETGgGEGV photo- Q00169 G5(CW_Ce!e_SiC2N3) transfer protein alpha 1283.058 1.58 Jurkat EVLVNEPYEK.FD] celecoxib 5 isoform T10(CW_minimalist_Si2N [KJ.EMNDAAMFYt 3); Adeny!yl cyclase- Q01518 987.9608 2.66 K562 tag Nr.[V] R12(CW_minimalist_Si2N associated protein 1 3) [RJ.gMPPPLRGG G1(CW_Nap_SiC2N3); RNA-binding protein photo- Q01844 PGGPGGPGGPM 1414.184 2.69 Jurkat M23(Oxidation) EWS naproxen 4 GRmGGR.[G]

Q05639; [KJ.THiNiVVIGHV l3(CW_Nap_SiC2N3); Elongation factor 1- photo- 1249.158 1.48 (562 P68104 DSGK.fS] l5(CW_Nap_SiC2N3) alpha 2 naproxen 4

Complement [KJ.VEEQEPELTS component 1 Q photo- Q07021 V18(CW_Nap_SiC2N3) 1371 .193 3.02 Jurkat TPNFVVEviK.FN] subcomponent-binding naproxen 4 protein, mitochondrial

[Rj.ERSTPSLPC MlO(Oxidation); A-kinase anchor protein photo- Q12802 mVSAQDAPLPK 1267 6 3.24 Jurkat R31(Cwlcele_SiC2N3) 13 ceiecoxib 5 GADLIEEAASr . l

Aminoacyl tRNA [KJ.HNAVNATLID synthase complex- Q13155 SWVDIAIfQLKEG F18(CW_Cele_SiC0N3) 1219.59 3.09 Jurkat interacting celecoxib 5 SSKEK.FA] multifunctional protein 2

[K].eGSVWDLAA NAD(P) Q13423 EAGGNFETTKP E 1(CW_Cele_SiC2N3) transhydrogenase, 1738.83 2.4 K562 celecoxib 5 GELYIHK.[G] mitochondrial [RJ.SLGVGYAAV NAD(P) N 1 1(CW_Cele_SiC2N3) photo- Q13423 DnPIFYKPNTAm transhydrogenase, 1172.24 3.14 Jurkat M21 (Oxidation) celecoxib LLGDAKK.[T] mitochondrial [KJ.SvCKAPELLA photo- 0.13617 V2(CW_Cele_SiC2N3) Cullin-2 852.4174 2.82 Jurkat K.[Y] ceiecoxib 5 [RJ.SIGYDLPmVE L2(CW_Nap_SiC2N3); Spectrin alpha chain, photo- Q13813 EGEPDPEFEAIL 1859.348 2.81 Jurkat M8(Oxidation) non-erythrocytic 1 naproxen 4 DTVDPNRJD] Q 3885; [R .A ILVDLePGT photo- E7(CW_Ce!e_SiC2N3) Tubulin beia-2A chain 1081 4.38 K562 P07437 DSVR.[S] celecoxib 5 Q 3885; [R .A LVdLEPGT photo- D5(CW_Cele_SiC2N3) Tubulin beta-2A chain 1081 1.8 K562 P07437 MDSVR. [S] ceiecoxib 5 Q 3885; [KJ. LTTPTYGDLN photo- PQ7437; HLVSATMSG VTT L24(CW_Nap__SiC2N3) Tubulin beia-2A chain 1553.268 2.8 K562 naproxen P68371 C!R. [F] Q 3885; [Kj. LTTPTYGDIN photo- PQ7437; HLVSATMSG VTT L9(CW_Nap_SiC2N3) Tubulin beta~2A chain 1553.268 3 .11 K562 naproxen 4 P68371 CLR. [F] Q 3885; [KJ. LTTPTYGDLN photo- P07437; HLVSATMSG VTT R25(CW_Nap_SiC2N3) Tubulin beia-2A chain 1553.264 3.36 K562 naproxen 4 P68371 CLr. [F] Q 3885; [K]. LTTPTYGDLN photo- P07437; HLvSATMSG VTT V 13(CW_Nap_SiC2N3) Tubulin beia-2A chain 1553.264 4.08 K562 naproxen 4 P68371 CLR. [F] Q13885; [KJ. LTTPTYGDLN photo- P07437; HLVSATMSG VTT R25(CW_Nap SiC2N3) Tubulin beta-2A chain 1553.265 2.68 K562 naproxen 4 P68371 CLr. [F] [KJ.QTDVLqQLSI Q6(CW_miniGL_SiON3); Cytoplasmic dynein 1 photo- Q14204 1106.555 2.57 Jur a QmANAK.[F] 12(Oxidation) heavy chain 1 glutarimide [Kj.dNQQKANEV D 1(CW_minimalist_Si2N3 Cytoplasmic dynein 1 Q 4204 979.991 3 2.91 K562 tag 7 EQ R . D] ) heavy chain 1 [R .EQWEpVfQN P5(CW_Nap_SiC2N3); photo- Q 14331 GKMALLASNSCF Protein FRG 1 1192.245 4 .1 Jurkat F7(CW_Nap_SiC0N3) naproxen 4 I .[C] [Rj. EQWEpVfQN P5(CW_Nap_SiC2N3); photo- Q 14331 GKMALLASNSCF Protein FRG 1 1192.247 3.53 Jurkat F7(CW_Nap_SiC0N3) naproxen 4 IR .[C] [KJ.SEKFQEAg EL photo- Q14690 G8(CW__Nap__SiC2N3) Protein RRP5 hornolog 10 12.982 2.55 Jurkat YNR. [M] naproxen 4 [R .ESEEKLKQQ Pre-mRNA-splicing photo- Q 15007 A 14(CW_Nap_SiC2N3) 1136.568 2.97 K562 QQESaR. [R] regulator WTAP naproxen 4

[Rj. HSQELPAl LD D 18(CW_minimalist_Si2N Condensin complex Q 1502 1 1156.079 2.68 K562 tag 7 DTTLSGSdRIN] 3} subunit 1 rm.SSIAGILLKAT photo- Q15149 L6(CW_Nap_SiC0N3) Plectin 2 949.0222 2.57 K562 NEK.[L] naproxen [R].SMVEEGTGL RLLEAAAqSTKG Q 17(CW_minimalist_Si2 Q15149 Plectin 3 1370.992 3.52 K562 taq 7 YYSPYSVSGSGS N3) TAGSR.[T] [RJ.SMVEEGTGLr LLEAAAQSTKGY R10(CW_minimalist_Si2N Q15149 Piectin 3 1370.993 3.47 K562 tag YSPYSVSGSGST 3) AGSR.[T] Non-POU domain- [RJ.eKLEMEMEA photo- Q15233 El (CW__Cele__SiC2N3) containing octamer- 627.9317 2.55 Jurkat AR.[H] celecoxib binding protein

[Rl.CSGIASAAAA Nicotinate-nucleotide photo- Q15274 AVEAARGAGWT H23(CW_Nap_SiC2N3) pyrophosphorylase 1051 .192 3 7 (562 naproxen GhVAGTRK.fT] [carboxyiating]

Microtubule-associatec [RJ.NiELIcQENEG l2(CW_Nap_SiC2N3); photo- Q15691 protein RP/EB family 1362.642 2.59 Jurkat ENDPVLQR.[i] C6(Carbamidomethyl) naproxen 4 member 1

Microtubule-associatec [RJ.NIELicQENEG l5(CW_Nap_SiC2N3); photo- Q15691 protein RP/EB family 1362.642 2.67 Jurkat ENDPVLQR.[I] C6(Carbamidomethyl) naproxen 4 member 1

[Kj.aFGNEWKQA A1(CW_minimalist_Si2N3 Tubulin-specific Q15813 2 843.4342 2.82 K562 taq 7 GGHK.[DJ ) chaperone E [RJ.LPAIpRSATN UDP-N- photo- GKSETITADVNH P5(CW_Ceie_SiC2N3) acetylhexosamine 1064.87 3.44 K562 ceiecoxib NLK.[DJ pyrophosphorylase [KJ.EGEEAGPGD Hsp90 co-chaperone photo- Q16543 PILEAVPKTGDEK L 11(CW_Nap_SiC0N3) 2 1345.654 2.57 K562 Cdc37 naproxen 4 D1 Phosphoenolpyruvate [KJ.dVARVESKTV photo- Q16822 D1(CW_miniGL_SiON3) carboxykinase [GTPJ, 2 1147.121 3.03 K565 IVTPSQRIDl glutarimide 8 mitochondrial Phosphoenoipyruvate [R].dEGWLAEHM photo- Q16822 D1(CW__Nap SiC2N3) carboxykinase [GTP], 2 1296.652 2.89 K562 L!LG!TSPAGK.[K] naproxen 4 mitochondrial [RJ.VAPDEHPILL photo- Q562R1 E12(CW_Cele__SiC2N3) Beia-actin-like protein 2 3 833.746 3.81 Jurk TeAPLNPK.il] ceiecoxib Q6DN03; Putative histone H2B photo- [R] !A HYNKR [S] L1(CW_Nap SiC2N3) 3 452.5765 2.25 K562 060814 type 2-C naproxen 4 [Rj.VGAGAPVYm M9(Oxidation); photo- Q F 13 AAVIEYLTAEILEL Histone H2A type 2-A 1164.905 2.62 Jurkat L13(CW__Cele_SiC0N3) celecoxib 5 AGNAAR.[D] [Rj.VGAGAPVYm M9(Oxidation); photo- G6FI13 AAVLEYLTAEiLE Histone H2A type 2-A 1164.905 4.24 Jurkat l20(CW Cele SiC0N3) celecoxib 5 LAG AA R [D] [RJ.VGAGAPVYM photo- G6FI13 AAVLEYLTAEiLE l20(CW Ceie SiC0N3) Histone H2A type 2-A 4 869.9286 3.13 Jurkat celecoxib 5 LAGNAAR.fD] [RJ.VGAGAPVYM photo- Q6FI13 AAVLEyLTAEILE Y 15(CW Cele SiC0N3) Histone H2A type 2-A 4 869.9293 5.55 Jurkat celecoxib 5 LAGNAAR.[D] [RJ.VGAGAPVYM photo- AAVLEYLTAelLE E19(CW__Cele__SiC0N3) Histone H2A type 2-A 4 869.9293 3.99 Jurkat celecoxib 5 LAGNAAR.[D] [RJ.VGAGAPVYM photo- Q6FI13 AAVLEYLTAelLE E 19(CW_ee!e__SiC0N3) Histone H2A type 2-A 1159.569 5.48 Jurkat ceiecoxib 5 LAGNAAR.fD] [RJ.VGAGAPVYM photo- Q6FI13 AAVLEYLTAelLE E 19(CW_ee!e__SiC0N3) Histone H2A type 2-A 1159.569 4.74 Jurkat ceiecoxib 5 LAGNAAR.[D] [RJ.VGAGAPVYM Q6F113 AAVLEYLTAEIIEL L21(C eie SiCQN3) Histone H2A type 2-A 4 869.9294 3.01 Jurkat celecoxib 5 AGNAAR.[D] [RJ.VGAGAPVYM Q6F 3 AAVLEYLTAelLE E 19(CW Cele SiC0N3) Histone H2A type 2-A 4 869.9294 5.07 Jurkat ceiecoxib 5 LAGNAAR.[D] [Rj.VGAGAPVYM AAVLEYLTAelLE photo- G6FI13 E19(CW_Cele SiC2N3) Hisione H2A type 2-A 4 991 .7477 4.45 Jur a LAG AA RDNKK [ celecoxib 5 T] [Rj.VGAGAPVYM G6FI13 AAVLEYLTAelLE E19(CW Ce!e_SiC0N3) Histone H2A type 2-A 4 869.93 4.65 Jurkat celecoxib 5 LAGNAAR.[D] [Rj.VGAGAPVYM Q6FI13 AAVLEYLTAelLE E19(CW Cele SiC2N3) Histone H2A type 2-A 3 1160.239 5.47 Jurkat ceiecoxib 5 LAGNAAR.[D] [Rj.VGAGAPVYM photo- G6FI13 AAVLEYLTAelLE E19{CW__Cele__SiC2N3) Histone H2A type 2-A 3 1160.246 3.3 Jurkat ceiecoxib LAGNAAR.[D] [Rj.VGAGAPVYm photo- M9(Oxidation); Q6FI13 aAVLEYLTAEILE Histone H2A type 2-A 1181 .923 1.99 Jurkat indomethacin A10(CW_lndo_SiC2N3) LAGNAAR.[D] 6 [Rj.VGAGAPVYm photo- M9(Oxidation); Q6FI13 AAVLEYLTAelLE Histone H2A type 2-A 1181 .923 5.57 Jurkat indomethacin E19(CW_lndo_SiC2N3) LAGNAAR.fD] [Rj.VGAGAPVYM photo- G6FI13 AAVLEYLTAelLE E19(CW_lndo_SiC0N3) Histone H2A type 2-A 4 882.1964 4.09 Jurkat indomethacin LAGNAAR.fD] 6 [Rj.VGAGAPVYM photo- Q6FI13 AAVLEYLTAelLE E19(CW_lndo_SiC0N3) Histone H2A type 2-A 4 882.2015 4.96 Jurkat indomethacin LAGNAAR.[Dj 6 [Rj.VGAGAPVYM photo- G6FI13 AAVLEYLTaEILE A18(CW_lndo_SiC2N3) Histone H2A type 2-A 4 882.7021 3.98 Jurkat indomethacin LAGNAAR.fD] [Rj.VGAGAPVYM AAVLeYLTAEILE photo- G6FI13 E14(CW_Nap_SiC0N3) Hisione H2A type 2-A 5 775.0067 7 Jurkat LAGNAARDNKK.[ naproxen T] photo- Q6FI13 AAVLEYLTAEILE P6(C Nap SiC0 3) Histone H2A type 2-A 3 1129.255 2.4 Ju naproxen LAG AA R D] [Rj.VGAGAPVYM photo- G6FI13 AAVLEYLTAEiLE !20(CW_Nap._SiCQN3) Histone H2A type 2-A 129.255 4.87 Jurkat naproxen 4 LAGNAAR.[D] [R].FQSSAVmAL M7(Oxidation); QEAsEAYLVGLF photo- Υ 7 . S13(CW_Cele_SiC2N3); Histone H3.2 1358.954 6.71 K562 \ U EDTNLcAIHAK.[R celecoxib 5 C27(Carbamidomeihyl) j Q71 U36; [Rj.AVFVdLEPTVi phoio- D5(CW_Cele_SiC2N3) Tubulin alpha-1A chain 2 124.033 3 2 K562 Q9BQE3 DEVR.[T] ceiecoxib 5 Q71 U36; [Rj.AVFVDLEpTV P8(CW Cele SiC2N3) Tubulin alpha-1A chain 2 1124.033 3.79 K562 Q9BQE3 IDEVR.[T] ceiecoxib Q71 U36; [Rj.AVFVDLEPTvi photo- V10(CW_Cele_SiC2N3) Tubulin aipha-1A chain 1124.033 2.45 K562 Q9BQE3 DEVR.[T] celecoxib Q71 U36; [Rj.AVFVDLEpTV photo- P8(CW_Cele_SiC2N3) Tubulin alpha-1A chain 1124.032 3.43 K562 Q9BQE3 IDEVR.[Tj ceiecoxib

Q71 U36; [KJ.TIGGGDDSFN photo- F13(CW__Ceie__SiC2N3) Tubulin aipha-1A chain 1277.024 2.68 Jurkat Q9BQE3 TFfSETGAGK [H] celecoxib

Q71 U36; [Rj.AVFVdLEPTVI D5(CW__Cele_SiC2N3) Tubulin alpha-1A chain 1124.034 3.66 Jurkat Q9BQE3 DEV R.p ceiecoxib 5 Q71 U36; [Rj.AVFvDLEPTVI photo- V4(CW_Ceie__SiC2N3) Tubulin aipha-1A chain 1124.034 2.25 Jurkat Q9BQE3 DEVR.[Tj celecoxib 5 Q7 U36; [Rj.AVFVDLEpTV photo- P8(CW_Cele_SiC2N3) Tubulin alpha-1A chain 2 1124.035 2.86 Jurkat Q9BQE3 IDEVR.[Tj ceiecoxib 5 Q71 U36; [Rj.AVFVDLEpTV P8(CW Ceie SiC2N3) Tubulin alpha-1A chain 2 1124.035 2.67 Jurkat Q9BQE3 IDEVR.[Tj ceiecoxib 5 photo- Q71 U36; [Rj.AVFVDLePTV E7(CW_lndo_SiC2N3) Tubulin aipha-1A chain 2 1148.569 2.54 Jurkat indomethacin Q9BQE3 IDEVR.[Tj 6 photo- Q7 U36; [Rj.AVFvDLEPTVI V4(CW_lndo_SiC2N3) Tubulin alpha-1A chain 2 1148.569 1.57 Jurkat indomethacin Q9BQE3 DEVR.fTj

Q71 U36; [Kj.TIGGGDDSFN photo- K20(CW_Nap_SiC2N3) Tubulin aipha-1A chain 2 1231 .56 2.94 K562 Q9BQE3 TFFSETGAGklHj naproxen Q71 U36; [K].TIGGGDDSFN photo- F12(CW_Nap_SiC2N3) Tubulin aipha-1A chain Q9BQE3 TfFSETGAGKIHI naproxen

Q7 U36; [K] T GGGDDSFN photo- F13(CW_Nap_SiC2N3) Tubulin aipha-1A chain Q9BQE3 TFfSETGAGK.FH] naproxen

Q7 U36; [Rj.lHFPLATYAP Q9BQE3; K16(CW_Cele_SiC2N3) Tubulin aipha-1A chain VISAEk.[A] ceiecoxib 5 P68366 Q7 U36; [Rj.lHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin alpha-1A chain 2 1151 .564 1.93 K562 VISAeK.[A] ceiecoxib P68366 Q71 U36; [Rj.lHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin aipha-1A chain 3 768.0456 4.76 K562 VISAeK.[A] ceiecoxib P68366 Q71 U36; [Rj.lHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin aipha-1A chain 3 768.0456 2.53 K562 VISAeK.[A] celecoxib 5 P68366 Q7 U36; [Rj.lHFPLATYAP photo- Q9BQE3; K16(CW_Cele_SiC2N3) Tubulin alpha-1 A chain 2 1151 .563 3.78 K562 VISAEk.fA] celecoxib 5 P68366 Q7 U36; [Rj.lHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin alpha-1A chain 3 768.0442 VISAeK.[A] celecoxib 5 P68366 Q71 U36; [Rj.lHFPLATYAP photo- Q9BQE3; K16(CW_Cele_SiC2N3) Tubulin alpha-1A chain 2 1151 .561 3.14 K562 VISAEk.[Aj celecoxib 5 P68366 Q7 U36; [Rj.lHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin alpha-1 A chain VISAeKIA] celecoxib 5 P88366 Q71 U36; [Rj.lHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin alpha-1 A chain VISAeKIA] celecoxib 5 P68366 Q71 U36; [K].VGINYQPPTV Q9BQE3; P12(CW_Cele_SiC2N3) Tubulin alpha-1A chain 2 1185.572 3.35 Jurkat VpGGDLAK.[Vj ceiecoxib 5 P68366 Q71 U36; [R].IHFPLATYAP photo- Q9BQE3; K16(CW_Cele_SiC2N3) Tubulin aipha-1A chain 2 1151 .564 2.4 Jurkat ViSAEk.[A] ceiecoxib 5 P68366 Q71 U36; [RJ .IHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin aipha-1A chain VISAeK.[A] ceiecoxib 5

Q71 U36; [Rj.lHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin alpha-1A chain 3.87 Jurkat VISAeK.[A] celecoxib 5 P68366 Q71 U36; [RJ.IHFPLATYAP photo- Q9BQE3; E15(CW_Cele_SiC2N3) Tubulin alpha-1A chain 768.0471 2.19 Jurkat VISAeK.[A] celecoxib P68366 Q7 U36; photo- [K].VGINYQPPTV Q9BQE3; K18(CW_lndo_SiC2N3) Tubulin alpha-1A chain 1210.108 2.48 Jurkat indomethacin VPGGDLAk.[V] P68366 [KJ.SATLCSLPSc C 10(Carbamidomethy!); Elongation factor-like photo- Q7Z2Z2 PPF!PLNFEaTPI 2 1592.809 1.5 K562 A20(CW_Nap_SiC2N3) GTPase 1 naproxen 4 VR.[V] [Rj.EAQAALAeA photo- Q7Z406 QEDLESERVART E8(CW_Cele_SiC2N3) Myosin- 14 3 987.4627 3.48 Jurkat ceiecoxib 5 K.[A] [Rj.tELGLDLGLE photo- Q86UE4 T1(CW_Cele_SiC2N3) Protein LYRIC 2 915.4362 2 1 K562 PK.[R] celecoxib 5 [KJ.RASYGHsMV S7(CW_Nap_SiC0N3); photo- Q86X76 VDPWGTWARcs C20(Carbamidornethyl); Nitrilase homolog 1 3 1379.334 3.43 Jurkat naproxen 4 EGPGLCLAR.[I] S21(CW_Nap_SiC0N3)

[KJ.RASYGHsMV S7(CW_Nap_SiC0N3); photo- Q86X76 VDPWGTWARcs C20(Carbamidomethyl); Nitrilase homolog 1 3 1379.334 3.41 Jurkat naproxen 4 EGPGLCLAR.[I] S21(CW_Nap_SiC0N3) [RJ.VGAGAPVYL Q8IUE6; AAViEYLTAEILEL photo- P04908; L13(CW_Cele_SiC0N3) Histone H2A type 2-B 5 789.6063 7.2 Jurkat AGNAARDNKK.[T celecoxib 5 P16104 ] [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAelLE photo- P04908; E19(CW_Cele SiC0N3) Hisione H2A type 2-B 4 986.7543 6.13 Jurkat LAG AA RDNKK [ celecoxib 5 P16104 T] [Rj.VGAGAPVYL Q8IUE6; AAVLEyLTAE!LE photo- P04908; Y15(CW Ceie SiC0N3) Histone H2A type 2-B 4 954.7305 5.61 Jurkat LAGNAARDNK.TK celecoxib 5 P16104

Q8iUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYITAE!LEL L16(CW_Cele__SiC0N3) Histone H2A type 2-B 4 954.7305 4.67 Jurkat celecoxib 5 P16104 AGNAARDNK.[Kj Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AaVLEYLTAEILE A 11{CW__Cele__SiC0N3) Histone H2A type 2-B 4 865.4364 4.37 Jurkat celecoxib P16104 LAGNAAR.[Dj Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLtAEI LEL T 17(CW_Cele__SiC0N3) Histone H2A type 2-B 1153.591 2.18 Jurk celecoxib 5 P16104 AGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLeYLTAE!LE E14(CW_Cele SiC0N3) Histone H2A type 2-B 3 1153.591 4.34 Jurkat celecoxib 5 P16104 LAG AA R [D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CW_Cele SiC0N3) Histone H2A type 2-B 4 865.4404 6 1 Jurkat celecoxib 5 P16104 LAGNAAR.[D] Q8iUE6; [Rj.VGAGAPVYL photo- AAVLEYLTAelLE E19(CW Ceie SiC0N3) Histone H2A type 2-B 4 865.4404 4.06 Jurkat celecoxib 5 P16104 LAGNAAR.[Dj Q8iUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E 19(CW__Ceie__SiC0N3) Histone H2A type 2-B 1153.584 6.22 Jurkat celecoxsb 5 P16104 LAGNAAR.[Dj Q8IUE6; [Rj.VGAGAPVYL photo- AAVLEYLTAelLE E 19(CW_ee!e__SiC0N3) Histone H2A type 2-B 1153.584 3.76 Jurkat celecoxsb 5 P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- AAVLEYLTAelLE E19(CW__Ce!e_SiC0N3) Histone H2A type 2-B 4 865.4385 4.23 Jurkat ceiecoxib 5 P16104 LAG AA R D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CW_Cele_SiC0N3) Histone H2A type 2-B 3 1153.581 4.12 Jurkat ceiecoxib 5 P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAvLEYLTAE!LE V12(CW_Cele_SiC0N3) Histone H2A type 2-B 4 865.4391 2.91 Jurkat celecoxib 5 P16104 LAGNAAR.[D] Q8IUE6: [Rj.VGAGAPVYL photo- AAVLEYLTAelLE E 19(CW_Cele_SiC0N3) Histone H2A type 2-B 4 865.4391 5.23 Jurkat celecoxib 5 P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLTAelLE E19(CW_Cele_SiC0N3) Hisione H2A type 2-B 4 865.4399 3.58 Jurkat celecoxib P16104 LAG AA R [D] Q8IUE6; [Rj.VGAGAPVYL pboto- P04908; AAVLEYLTAelLE E 19(CW_Cele_SiC2N3) Histone H2A type 2-B 3 1154.253 3.88 JurkE ceiecoxib 5 P16104 LAGNAAR.[D] [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAelLE pboto- P04908; E19(CW_Cele_SiC0N3) Histone H2A type 2-B 5 789.6062 6.41 Jurkat LAGNAARDNKK.[ ceiecoxib 5 P16104 T] [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAEIIEL photo- P04908; L21(CW_Cele_SiC0N3) Histone H2A type 2-B 5 789.6062 4.27 Jurkat AGNAARDNKKJT celecoxib 5 P16104 [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAelLE photo- PQ4908; E19(CW_Cele_SiC0N3) Histone H2A type 2-B 4 986.7557 6.25 Jurkat LAGNAARDNKK.[ celecoxib 5 P16104 T] [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAelLE pboto- P04908; E19(CW_Cele_SiC0N3) Hisione H2A type 2-B 4 986.7557 4.05 Jurkat LAGNAARDNKK.[ ceiecoxib 5 P16104 T] [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAelLE photo- P04908; E19(CW_Cele_SiC0N3) Histone H2A type 2-B 4 986.7576 3.66 Jurkat LAGNAARDNKK.[ celecoxib 5 P16104 T] [RJ.VGAGAPVYL Q8IUE6; AAVLEYLTAelLE phoio- P04908; E19(CW_Cele__SiC0N3) Histone H2A type 2-B 4 954.7284 4.52 Jurkat LAGNAARDNK.[K celecoxib 5 P16104 J G81UE6; [Rj.VGAGAPVYL P04908; AAVLEYITAEILEL L16(CW_Cele_ SiCONS) Histone H2A type 2-B 4 865.4403 5.59 Jurkat celecoxib 5 P16104 AGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL P04908; AAVLEYLTAelLE E19(CW_Cele__SiC0N3) Histone H2A type 2-B 4 865.4403 7.23 Jurkat ceiecoxib 5 P16104 LAGNAAR.[Dj Q8IUE6; [RJ.VGAGAPVYL photo- P04908; AAVLEYLTAei LE E19(CW_Cele__SiC0N3) Histone H2A type 2-B 3 153.586 5.14 Jurkat ceiecoxib 5 P16104 LAGNAAR.[D] Q8iUE6; [RJ.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CW_Cele. _SiC0N3) Histone H2A type 2-B 3 1153.586 6.56 Jurkat ceiecoxib 5 P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLeYLTAE!LE E14(CW_Cele. _SiC2N3) Histone H2A type 2-B 3 1154.25 6.12 Jurkat ceiecoxib 5 P16104 LAG AA R [D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CW_Cele. _SiC2N3) Histone H2A type 2-B 3 154.257 5.82 Jurkat celecoxib 5 P16104 LAGNAAR.[Dj Q8IUE8; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CW_Cele. _SiC2N3) Histone H2A type 2-B 4 865.9426 6.1 1 Jurkat celecoxib 5 P 6 04 LAGNAAR.[Dj Q8IUE6; [Rj.VGAGAPVYL phoio- P04908; AAVLEYLTAelLE E19(CW_Cele_SiC2N3) Histone H2A type 2-B 3 1154.25 5.42 Jurkat celecoxib 5 P16104 LAGNAAR.[Dj Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLtAEILEL T17(CW_Ceie _SiC2N3) Histone H2A type 2-B 3 1154.25 5.25 Jurkat ceiecoxib 5 P16104 AGNAAR.fD] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLeYLTAEILE E14(CW_Cele. _SiC0N3) Histone H2A type 2-B 3 1153.585 5 Jurkat celecoxib 5 P16104 LAGNAAR.iDJ Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLTAeiLE E19(CVV_Ce!e__SiC2N3) Histone H2A type 2-B 3 154.258 5.24 Jurkat celecoxib 5 P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAeiLE E19(CVV_Ce!e__SiC2N3) Histone H2A type 2-B 3 1154.249 4.32 Jurkat celecoxib 5 P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL PQ4908; AAVLeYLTAEILE E14(CW Ce!e SiC2N3) Histone H2A type 2-B 3 1154.25 4.18 Jurkat ceiecoxib 5 P16104 LAGNAAR.[Dj Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEyLTAEILE Y15{CVV_Ceie SiC0N3) Histone H2A type 2-B 3 1153.581 3.13 Jurkat celecoxib 5 P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAeiLE E 9(CW_Cele_SiC0N3) Histone H2A type 2-B 4 865.4403 3.57 Jurkat celecoxib 5 P16104 LAGNAAR.[D] [Rj.VGAGAPVYL Q8IUE6; AAVLeYLTAEILE photo- P04908; E14(CW Ce!e_SiC0N3) Histone H2A type 2-B 4 986.7581 3.53 Jurkat LAGNAARDNKK.[ ceiecoxib 5 P16104 T] Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLTAEI!EL L21(CWJndo_SiC2N3) Histone H2A type 2-B 3 1170.61 4.1 Jurkat indometbacin P16104 AGNAAR.[Dj 6 Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLTAE!!EL L21(CWJndo__SiC2N3) Histone H2A type 2-B 3 1170.604 4.49 Jurkat indomethacin P16104 AGNAAR.[Dj 6 Q8IUE6; [Rj.VGAGAPVYL pboto- P04908; AAVLEYLtAEILEL T17(CWJndo__SiC2N3) Histone H2A type 2-B 4 878.2073 4.58 Jurkat indornethacin P16104 AGNAAR.[Dj 6 Q8IUE6; [Rj.VGAGAPVYL pboto- PQ4908; AAVLEYLTAEILE l20(CWJndo__SiC2N3) Histone H2A type 2-B 4 878.2073 4.78 Jurkat indometbacin P16104 LAGNAAR.[Dj 6 Q8IUE6; [Rj.VGAGAPVY ' L pboto- PQ4908; AAVLEYLtAEILEL T17(CWJndo_SiC2N3) Histone H2A type 2-B 4 878.2075 3.34 Jurkat indomethacin P 6 04 AGiMAAR.[D] 6 Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CWJndo__SIC2N3) Histone H2A type 2-B 4 878.2075 4.25 Jurkat indornethacin P16104 LAGNAAR.fD] 6 Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYITAEILEL L16(CWJndQ SiC2N3) Hisione H2A type 2-B 3 1170.607 3.09 Jurkat indomethacin P16104 AGNAAR.[D] 6 Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLTAelLE E19(CWJndo_SiC2N3) Histone H2A type 2-B 3 1170.607 4.95 Jurkat indomethacin P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTaEILE A18(CWJndo__SIC2N3) Histone H2A type 2-B 578.2087 4.9 Ju indornethacin P16104 LAGNAAR.fD] [Rj.VGAGAPVYL Q8IUE6; AAVIEYLTAEILEL photo- PQ4908; L13(CW_Nap_SiC0N3) Histone H2A type 2-B 5 771 .4151 8.32 Jurkat AGNAARDNKK.[T naproxen 4 P16104 ] [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAEILE photo- PQ4908; l20(CW__Nap__SiC0N3) Hisione H2A type 2-B 5 771 .4151 4.19 Jurkat LAGNAARDNKK.[ naproxen P16104 Tj [Rj.VGAGAPVYL Q8IUE6; AAVLEYLTAelLE photo- PQ4908; E19(CW__Nap__SiC0N3) Histone H2A type 2-B 4 931 .9976 4.15 Jurks LAGNAARDNKJK naproxen 4 P16104

[Rj.VGAGAPVYL Q8IUE6; AAVLEYITAEILEL photo- P04908; L16(CW_Nap_SiC0N3) Histone H2A type 2-B 5 771 .4146 7.78 Jurkat AGNAARDNKK.rr naproxen 4 P16104 [Rj.VGAGAPVYL Q8IUE6: AAVLEYLTAEILE photo- 20(CW_Nap_SiC0N3) Histone H2A type 2-B 5 771 .4146 4.4 Jurkat LAGNAARDNKK. naproxen 4 P16104 T] Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLtAEILEL T17(CW_Nap_Si' Histone H2A type 2-B 4 842.7067 3.56 Jurkat naproxen 4 P16104 AGNAAR.[Dj [RJ.VGAGAPVYL Q8IUE6; AAVLEYITAEILEL photo- P04908; L16(CW_Nap_SiC0N3) Hisione H2A type 2-B 4 964.0181 3.93 Jurkat AGNAARDNKK.fT naproxen 4 P16104 ] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CW_Nap_SiC0N3) Histone H2A type 2-B 4 842.706 4.06 Jurkat naproxen 4 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLTAelLE E19(CW_Nap_SiC0N3) Histone H2A type 2-B 4 842.702 5.79 Jurkat naproxen P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYLTAelLE E19(CW_Nap_SiC0N3) Hisione H2A type 2-B 4 842.702 3.91 Jurkat naproxen P16104 LAGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- PQ4908; AAVLEYITAEILEL L16(CW_Nap_SiC0N3) Histone H2A type 2-B 1123.264 2.13 Jurks naproxen 4 P16104 AGNAAR.[D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E 19(CW_Nap_SiC0N3) Histone H2A type 2-B 1123.264 5.42 Jurkat naproxen 4 P16104 LAG AA R [D] Q8IUE6; [Rj.VGAGAPVYL photo- P04908; AAVLEYLTAelLE E19(CW_Nap_SiC0N3) Histone H2A type 2-B 4 842.7052 4.04 Jurkat naproxen 4 P16104 LAGNAAR.fD] Q8IUE6: [Rj.VGAGAPVYL photo- AAVLEYLTAelLE E 9(CW_Nap SiC0N3) Histone H2A type 2-B 4 842.7052 5.14 Jurkat naproxen 4 P16104 LAGNAAR.[Dj [KJ.NcLLLITYLISE C2(Carbamidomethyi); photo- Q8NCA5 LEAARmLCVNAP L6(CW__Cele__SiC2N3); Protein FAM98A 1212.272 3.19 Jurkat ceiecoxib 5 PKK.[A] M18(Oxidation) [KJ.NASDMPeTIT Minor histocompatibility photo- Q8TCT9 E7(CW_Cele_SiC2N3) 933.887 3.6 Jurkat SR.[D] antigen H13 celecoxib 5

[KJ.NASDMPeTIT Minor histocompatibility photo- Q8TCT9 E7(CW__Ceie__SiC2N3) 2 933.8876 3.28 Jurkat SR. D antigen H13 ceiecoxib 5 photo- [Kl.NASDMPeTIT « , Minor histocompaiibslity Q8TCT9 D E7(CW_lndo_S.C2N3) g 3 958.4179 2.59 Jurkat indomethacin 6 photo- [KJ.NASDMPETiT Minor histocompatibility Q8TCT9 !9(CW_lndo_SiC2N3) 958.4179 1.55 Jurkat indomethacin SR.fD] antigen H 3

Zinc finger CCCH [KJ.EDEISLeDLIE photo- Q8WU90 E7(CW_miniGL_SiON3) domain-containing 2 1077.517 2.7 K562 RER. S g!utarimide 8 protein 15 [RJ.eDSNLEsSQL E1(CW_Nap_SiC2N3); photo- YP5 TVQAEFDMSAiP Protein ELYS 2 1737.322 2.47 Jurk S7(CW_Nap_SiC0N3) naproxen 4 R.[K] [KJ.LDPtKTTLLK photo- Q92597 MADCGGLPQ!S T4(CW_lndo_SiC2N3) Protein NDRG1 3 1074.213 3.28 Jurkat indomethacin QPAK.[L] [RJ.TLGDLVRKIG eiF-2-a!pha kinase photo- Q92616 L9(CW_Nap_SiC0N3) 2 890.9987 1.64 K562 EK.[I] activator GC naproxen 4 [RJ.TLGDLvRKLG e!F-2-alpha kinase photo- Q92616 V6(CW_Nap_SiC0N3) 2 890.9999 1.7 K562 -4 EK.[i] activator GC naproxen 4 [RJ.ATEKAFGqNS photo- DNA repair 92889 GWLFLDSSTSM Q8(CW_lndo_SiC2N3) 1158.216 3.26 Jurkat indomethacin endonudease XPF FINAR.[A] [KJ.DFIILSCVrAN Regulator of nonsense photo- Q92900 EHQGIGFLNDPR R9(CW_Nap_SiC2N3) 3 1023.526 1.87 Jurkat transcripts naproxen 4 photo- [RJ.EsVFTVEGG Q99623 S2(CW_lndo_SiC2N3) Prohibitin-2 3 604.6122 1.81 K562 indomethacin HR. A]

[KJ.SvVaKFNASQ V2(CW_lndo_SiC2r Q99623 Prohibitin-2 950.1399 2.08 Jurkat indomethacin LITQR.[A] A4(CW__lndo__SiC0N3)

[KJ.VAVPSTIHCD photo- Aconifate hydratase, HLIEAQVGGEk.[ K21(CW_lndo_SiC0N3) 1398.163 2.44 (562 indomethacin mitochondrial Dehydrogenase/reducta [R] .aW NSVR AS photo- Q9BTZ2 A1(CW miniGL_SiQN3) s SDR family member 981 .4587 1.37 Jurkat SGMTR.[R] glutarimide 8

[Rj.SGPFGQLFR photo- Q9BUF5 PDNFIFgQTGAG G16(CWJndo__SiC2N3) Tubulin beta-6 chain 1710.796 2.98 Jurkat indomethacin NNWAK.[G]

M (Oxidation); [Rj.ALTVPELTQQ M17(Oxidation); photo- Q9BUF5 mFDARNmMAAc Tubulin beta-6 chain 1200.893 3.52 K562 C2 (Carbamidomethyl); naproxen 4 DPRhGR.[Y] H25(CW__Nap__SiCGN3)

[KJ.IGEmPLTDSIL M4(Oxidation); Acetyi-CoA photo- CDGLTDAFHNcH Q9BWD1 C22(CW_indo_SiCQN3); acetyitransferase, 1423.637 3.65 K562 indomethacin mGITAENVAKK.[ M24(Oxidation) cytosolic W] [K].KEYSLdTR.[G W D repeat-containing photo- Q9GZS3 D6(CW__miniGL_SiON3) 710.35 1.36 Jurkat ] protein 6 1 glutarimide 8 [Rj.SVGViSPYRK Putative helicase OV- photo- Q9HCE1 l5(CW_Ceie__SiC0N3) 824.9018 2.35 K562 [Q] 10 ceiecoxib 5 photo- [Kl.QWKhLPKIA Putative helicase OV- Q9HCE1 H5(CWJndoj3iC2 771 .9201 3.04 Jurkat indomethacin 10 6 photo- [K].QWKhLPK.[A Putative helicase OV- Q9HCE1 H5(CW_indo_SiC2N3) 771 .9197 2.6 Jurkat indomethacin 10 ] 6 [Rl.GYENHIFVGS 28S ribosomai protein phoio- Q9NP92 KtADPCCYGHTQ T12(CVV_Nap_ SiC2N3) 1268.274 3.86 K562 S30, mitochondrial naproxen 4 FHLLPDK.FL]

[Rj.sDAGLESDTA S1(CW__minimalist__Si2N3 Nucleolar RNA helicase Q9NR30 1091 .034 3.09 K562 tag 7 mKKGETLR.[K] ) ; M 11(Oxidation) 2

14 kDa photo- [R].SGAPAAeSK E7(CW_lndo_SiC2N3); Q9NRX4 phosphohistidine 1425.172 2.52 K562 indomethacin E VRGYk W] K16(CW_indo_SiC0N3) phosphatase O CM CN CN O CM CN CN CN CN CN

CN CN

O O ca CN CN co o o a < ϋ Φ _g co CO - c S c E Q . a. r s O c Φ O CD Φ CO 3 3 c c o g co ca c o c c x x o £ O - Q x E a . co : O - o E co o- o CO O o *+ g o O O 3 o E Φ o ≤ x

O CM CD CN M ~ 5 Li > > Ν Ν 3 Q X X Z 3 3 σ> σ σ σ σ a σ σ σ [K].IDQQQQQKV G cw Cele SiC0N3); Histone-lysine N- Q - P ° - Q9UMN6 AASMPLSPG9Q ^Oxidation) m e thy!transferase 2B celecoxib 5 mEEVAGA\/K.[Q]

„ E7 C miniGL__SiON3); Structural maintenance . .

Q9UQE7 e L E13(CW_miniGL_SiON3); of chromosomes 3 1008.169 3.53 K562 m d R15(CW miniGL_ Si2N3) protein 3

[Rj.lSASGPeSLL ;7 , Inner nuclear Q9Y2U8 GGPGGASAAPA membrane protein 976.1482 1.44 K562 aGSK.[V] - _ ~

n r n d r [Rj.lSASGPeSLL ί , h t Q9Y2U8 SAA P membrane protein 3 976.1461 1.42 K562 aGSK.jVj ivlanl

Q9Y6C9 KGEELGPGNVQ H4(CW_Cele_SiC2N3) 3 6 7 4 3 ce ecox b 5 K.[E]

Q9Y6C9 K E L P 4 CW.Ce te S C N3) .[E] y References (1) Lounkine, E.; Keiser, M. J.; Whitebread, S ; Mikhailov, D.; Hamon, J.; Jenkins, J . L.; Lavan, P.; Weber, E.; Doak, A . K.; Cote, S.; Shoichet, B . K.; Urban, L . Nature 2012, 486, 361.

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Supplemental Information Methods |0178| General Experimental Procedures . All reactions were performed in single-neck, oven- dried, roundbottomed flasks fitted with rubber septa under a positive pressure of nitrogen, unless otherwise noted. Air- and moisture-sensitive liquids were transferred via syringe or stainless steel cannula. Organic solutions were concentrated by rotary evaporation at 30-33 °C. Normal and reverse phase flash-column chromatography was performed as described by Still and co-workers. 1 Normal phase purifications employ silica gel (60 A, 40-63 µη particle size) purchased from Silicycle (Quebec, Canada). Analytical thin-layer chromatography (TLC) was performed using glass plates pre-coated with silica gel (0.25 mm, 60 A pore size) impregnated with a fluorescent indicator (254 nm). TLC plates were visualized by exposure to ultraviolet light (UV), iodine (I2), and/or submersion in ninhydrin followed by brief heating with a heat gun (10-15 seconds). [0179] Chemical Materials . Commercial solvents and reagents were used as received with the following exceptions. Dichlorom ethane and N,N-dimethylformamide were purified according to the method of Pangborn and co-workers. 2 Triethylamine was distilled from calcium hydride under an atmosphere of nitrogen immediately before use. 3-aminopiperidine-2,6- dione hydrochloride was obtained from Ark Pharm. RapiGest was prepared according to the method of Lee and co-workers.' 3-[4-({Bis[(l-tert-butyl-lH-l,2,3-triazol-4- yl)methyl]amino}methyl)-lH-l,2,3-triazol-l-yl]propanol (BTTP) was prepared according to the method of W u and co-workers. 4 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was obtained from Sigma Aldrich. Biotin-CA(PEG) -alcohol S 4 was synthesized according to the method of Tirrell and co-workers 5 [0180 Biological Materials . COX-2 polyclonal antibody (PAS- 168 17), histone H2A polyclonal antibody (PA5-35893) and high sensitivity streptavidin-HRP (21 30) were purchased from Thermo Fisher Scientific and used in 1:100, 1:500 and 1:10,000 dilutions, respectively. Anti -Hi stone H2B monoclonal antibody (12364) was purchased from Cell Signaling Technology and diluted to 1:1000 in Western Blot detection. Nucleophosmin (NPM1/B23) monoclonal antibody (sc-271737), Ku-70 (XRCC6) monoclonal antibody (sc- 56129), Ν ' Β p65 monoclonal antibody (sc-8008), Ly-GDI monoclonal antibody (sc- 376473), EF-1 a l monoclonal antibody (sc-21758), Cathepsin D monoclonal antibody (sc- 377299) and secondary antibody m-IgGK BP-HRP (sc-5 16102) were provided by Santa Cruz, and used in 1:500, 1:200, 1:500, 1:500, 1:100, 1:200 and 1 : 1000 dilutions, respectively. ONE-Gio Luciferase Assay System (E61 10) was purchased from Promega Corporation. [0181] Cell Culture Materials . K562 and Jurkat cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with

0% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37 °C and 5% C0 2 in a water-saturated incubator. EDTA-free protease inhibitor cocktail was obtained from Roche Diagnostics. Streptavidin-agarose beads were obtained from Thermo Scientific and washed with PBS prior to use. The GloResponse NF-KB-RE -1UC2P HEK293 Cell Line, a clonal derivative of Human Embryonic Kidney 293 (HEK293), was provided by Choudharv lab, and maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37 °C and 5% C0 2 in a water-saturated incubator [0182] Chemical Instrumentation . Proton nuclear magnetic resonance spectra (Ή MR) were recorded at 400 or 500 MHz at 24 °C, unless otherwise noted. Chemical shifts are expressed in parts per million (ppm, δ scale) downfield from tetram ethyl silane and are δ δ referenced to residual protium in the NMR solvent [CHC1 , 7.26; CHD 2OD, 3.31; (C ![) ) ( SCX δ 2.49]. Data are represented as follows: chemical shift, multiplicity (s = singlet, d =doublet, t = triplet, q =quartet, quin = quintet, m = multiplet and/or multiple resonances, br = broad, app = apparent), integration, coupling constant in Hertz, and assignment. Proton-decoupled carbon nuclear magnetic resonance spectra ( C MR) were recorded at 125 MHz at 24 °C, unless otherwise noted. Chemical shifts are expressed in parts per million (ppm, δ scale) downfieid from tetramethylsilane and are referenced to the carbon δ δ δ resonances of the solvent (CDCI3, 77 0; CD3OD, 49.0, (CD )2SO, 39.0). C NMR and data are represented as follows: chemical shift, carbon type. Chemical shifts are expressed in parts per million (ppm, δ scale) downfieid from tetramethylsilane. Infrared (IR) spectra were obtained using a Shimadzu 8400S FT- R spectrometer referenced to a polystyrene standard. Data are represented as follows: frequency of absorption (cm ), intensity of absorption (s = strong, m =medium, w =weak, br =broad). High-resolution mass spectrometry (HRMS) measurements were obtained at the Chemistry and Chemical Biology Department, Harvard University Mass Spectrometry Facility using a Bruker microTOF-Q II hybrid quadrupole- time of flight, Agilent 1260 UPLC-MS. Low-resolution mass spectrometry (LRMS) measurements were obtained on Waters ACQUITY UPLC equipped with SQ Detector 2 mass spectrometer. The samples were photoirradiated with UVP Blak-Ray B-100AP high- intensity L V lamp (UVP LLC, Upland, CA). The absorbance was measured on a multi-mode microplate reader FilterMax F3 (Molecular Devices LLC, Sunnyvale, CA). TAMRA- fluorescence and chemiluminescence were detected by scanning the gel on Azure Imager C600 (Azure Biosystems, Inc., Dublin, CA). Experimental Procedures with COX-2 [0183] COX-2 inhibitor screening assay by ELISA . The COX-2 inhibitor screening assay kit (701080, Cayman Chemical, Ann Arbor, MI) was used to determine the inhibitory concentration of COX-2 in the presence of photo-NSAIDs or NSAIDs. The effect of inhibitors on COX-2-mediated prostaglandin production was measured in triplicate with several concentration gradients of photo-NSAIDs or NSAIDs Non-specific binding (NSB), maximum binding (B0), 00% initial activity (IA), background COX-2 (BC) and blank samples, in duplicate, were also measured. A prostaglandin screening standard curve was obtained by plotting the data as n [B/Bo/(l-B/Bo)] versus log concentrations of prostaglandin and performing a linear regression fit. The concentration of prostaglandin for each inhibitor sample was calculated by using the prostaglandin standard curve. The curve of percent inhibition by the inhibitor concentration was fitted and analyzed to determine the IC50 value for inhibitors using GraphPad Prism (GraphPad Software, San Diego, CA). [0184] Competitive analysis of NSAIDs and photo-NSAIDs with isolated COX-2 . Recombinant human COX-2 (125 ng, 12036-H08B, Sino Biological Inc., Beijing, China) was separately incubated with each of the photo-NSAIDs with or without a 100-fold excess of the parent compound as a competitor for 2 hours at 37 °C. The samples were photo-irradiated for 30 minutes at 4 °C, tagged with TAMRA-azide (760765, Sigma-Aldrich, St. Louis, MO) by copper-click chemistry for 2 hours at 24 °C, and detected by fluorescence spectroscopy (Azure Imager C600, Azure Biosystems) with Cy3 excitation. 1 Molecular docking of the structure of COX-2 with photo-NSAIDs and the tag 7. The photo-NSAIDs, the parent compounds, and the tag 7 were structurally minimized using Gaussian 16 0 with a basis set of F 3-21g(d). The energetically minimal structures were used in a geometry-based molecular docking algorithm PatchDock (https ://bioinfo3d.cs.tau.ac.il/PatchDock/) to calculate docking transformations that based on a scoring function and atomic desolvation energy. The structures with the lowest desoivation energy and highest interface area size were used in Figure 13. The receptor molecule was obtained from the crystal structure of human COX-2 (PDB: 5KIR). [0186] In-vitro photolabeling of COX-2 with photo-NSAIDs and analysis by LC-MS/MS . Recombinant COX-2 ( 1 g) was separately incubated with each of the photo-NSAIDs (10

µΜ) or the tag 7 ( 0 µΜ) for 30 minutes at 37 °C, and photo-irradiated for 5 minutes at 4 °C. The samples were then tagged with the cleavable biotin azide probe 10 by copper-click chemistn,' for 3 hours at 24 °C, followed by sample digestion with trypsin for 12 hours at 37 °C, and probe cleavage with 2% formic ac . The resulting peptides were analyzed by LC- MS/MS. MS data was searched in Proteome Discoverer v2.2 with SEQUEST HT or Byonic v2.1 against the recombinant COX-2. Experimental Procedures with Whole Celts [0187] Cell growth assay (MTT) with photo-NSAIDs and NSAIDs . Jurkat cells were seeded in a 96-weli flatbottomed cell culture plate (Falcon) in RPM with 10% FBS and 1% penicillin/streptomycin at a density of 1 cells/mL and maintained for 24 hours at 37 °C and 5% C0 2 atmosphere. Cells were treated with photo-NSAIDs or NSAIDs in triplicate at different doses and incubated for 24 hours at 37 °C. MTT solution (10 , 5 mg/mL) was added to each well and gently mixed. The cells were incubated for 4 hours at 37 °C, followed by addition of 0.1 mL isopropanol with 0.04 N HC1 to each well. The resulting mixture was mixed thoroughly by repeated pipetting. The absorbance was measured within 1 hour on a multi-mode microplate reader with a wavelength of 620 nm. [0188] In-situ photo-labeling of K562 or Jurkat cells with photo-NSAIDs . K562 cells or PMA/Ionomycin activated Jurkat cells (-97% cell viability) were suspended in FBS-free RPMI at the indicated concentration of photo-NSAIDs or negative controls tag 7 the photo- glutarimide 8, or the analog 9 for 2 hours at 37 °C, followed by UV irradiation at 365 nm for 30 minutes at 4 °C. In competition experiments, cell lysates were co-treated with the photo- NSAIDs and their parent compounds in 10-fold excess. The photoirradiated samples were pelleted, lysed with 1% RapiGest and EDTA-free protease inhibitor and briefly sonicated with a probe tip sonicator. Sonicated cell lysates were cleared by centiifugation and the concentration of the soluble proteins was determined using the BCA protein assay. Protein

concentrations were adjusted to a final concentration of 2.5 mg/mL. Cell lysates (500 L ) were reacted with pre-mixed click reagents at a final concentration of 200 µΜ biotin azide probe 10, 300 µΜ copper (II) sulfate, 600 µΜ BTTP and 2.5 mM freshly-prepared sodium

ascorbate for 5 hours at 24 °C with rotation. The proteins were precipitated with methanol ( 1

mL) for 1 hour at -80 °C, pelleted by centiifugation (15,000 g) for 10 minutes at 4 °C, and air

dried for 10 minutes at 24 °C. [0189 Enrichment of photo-crosslinked proteins for LC-MS/MS . Biotinylated protein pellets were resuspended in 1% RapiGest in PBS (400 L) and briefly sonicated. Streptavidin-

agarose resin (200 ,uL, washed 3 χ 1 mL PBS) was added to the suspended proteins and incubated for 12 hours at 24 °C. The beads were centrifuged for 3 minutes at 3000 χ g and

the supernatant was removed. The beads were washed with 1% RapiGest ( 1 mL), urea (6M, 3 1 mL), and PBS (2 χ 1 mL) in succession. The washed beads were resuspended in PBS (200 L ) The proteins on beads were reduced with 5 mM dithiothreitol (DTT) for 30 minutes at 24 °C and alkylated with 0 mM iodoacetamide for 30 minutes at 24 °C in the dark. The beads were pelleted by centrifugation and resuspended in 0.5 M urea/PBS (200 L) and trypsin (1.5 g) digested for 12 hours at 37 °C with rotation. The supernatant digest was collected and the beads were

washed with PBS (200 µ ) and water (2 x 200 µ ). The washes were combined to obtain the "trypsin fraction". Cleavage of the probe 10 and recovery of the conjugated peptide was performed in 2% formic acid in water (200 L) for 30 minutes at 24 °C. The cleavage solution was collected and the beads were washed with 80% acetonitrile in water (400 L) and the fractions were combined to afford the "cleavage fraction". The trypsin and cleavage fractions were concentrated to dryness using a SpeedVac concentrator heated at 40 °C, and stored at -20 °C until analysis by LC-MS/MS.

[0190] Cell thermal shift assay (CETSA) with photo-NSAIDs and NSAIDs . Jurkat cells in 5

mL of FBSfree RPMI at a density of 2.5 χ 106 cells/mL were incubated with 50 _uM of tag 7, photo-NSAIDs or NSAIDs for 2 hours in a 5% C02 atmosphere at 37 °C. The cell suspension was then collected and centrifuged for 3 minutes at 300 χ g and the culture

medium was aspirated. The cell pellets were re-suspended and washed with PBS (2 χ 15 mL) by centrifugation. PBS ( I niL) supplemented with EDTA-free protease inhibitors ( 1x) was added to each tube, and the resulting cell suspension was equally distributed into eight different 0.2 mL PGR tubes. The PGR tubes were heated over a temperature gradient (37-62

°C) for 20 minutes in a 96-well thermal cycler, followed by repeated freeze-thaw cycles (5 ) . The PGR tubes containing the resulting cell lysates were centrifuged at 20,000 χ g for 30 minutes at 4 °C to pellet cell debris together with precipitated and aggregated proteins. Each supernatant with the soluble protein fraction was transferred carefully to a new tube and analyzed by Western blot. The Western blot bands were quantified by ImageJ, and the data were fitted to obtain apparent Tagg values using the Boltzmann Sigmoid equation within GraphPad Prism.

[0191] Luciferase reporter assay for NF- Β pathway . The GloResponse -KB - E -1UC2P HEK293 cell line contains a luciferase gene (luc2P) under the control of a minimal TATA promoter with multiple nuclear factor -κΒ response elements (NF-KB-RES). A total of 10,000

NF-KB-RE -1UC2P HEK293 cells per well were dispensed into a 384-well plate, and incubated respectively with 5 µΜ of tag 7, celecoxib (2), photoceiecoxib (5) and DMSO for 1 hour at 37 °C, followed by addition of two-fold serial dilutions of TNF-a to induce reporter gene expression. After 5 hours of induction in a tissue culture incubator at 37 °C, luminescence was quantified using the ONE-Glo Luciferase Assay System Reagent o a multi-mode microplate reader FilterMax F3 (read for 0.5 second/well). The TNF-a titration curve was fitted and analyzed to determine the half maximal effective concentration (ECso) using GraphPad Prism. Mass Spectrometry Procedures [0192] Mass spectrometry procedures . The desalted samples were resuspended in 0.1% formic acid in water (15 µ ) . The sample (4.0 _uL) was loaded onto a C18 trap column (3 cm, 3 µτη particle size CIO Dr. Maisch 150 µηι ID) and then separated on an analytical column (Thermo Scientific Acclaim PepMap 100, 2 µι particle size, 250 mm length, 75 urn internal diameter) at 150 nL/min with a Thermo Scientific EASY-nLC 1000 system connected in line to a Thermo Scientific Orbitrap Fusion Tribrid or Orbitrap Elite. The column temperature was maintained at 50 °C. The tryptic peptides were separated via a stepwise gradient from 5% to 98% of 0.1% formic acid in acetonitrile over 120 minutes (0- 1 minutes, 0-5%; 1-91 minutes, 5-27%, 91-1 15 minutes, 27-98%; 15-120 minutes, 98%-0%). The cleavage peptides were separated via a step-wise gradient from 5% to 98% of 0.1% formic acid in acetonitrile over 130 minutes (0-1 minutes, 0-5%, 1-81 minutes, 5-28%, 81-100 minutes, 28-98%; 100-135 minutes, 98%-0%). Survey scans of peptide precursors were performed at 120K FWHM resolution (m/z = 200). Tandem MS was performed on the most abundant precursors exhibiting a charge state from 2 to 5 at a resolving power settings of 15K and fragmentation energy of 36V. HCD/CID fragmentation was applied with 35% collision energy and resulting fragments detected using the normal scan rate in the ion trap. [0193] Data analysis procedures . Data analysis was performed with Proteome Discoverer v2.2 using SEQUEST HT, allowing for variable modifications (methionine oxidation: +15 995 Da; cysteine alkylation: +57.021 Da; photo-naproxen: +452 206 Da, +454.222 Da; photo-celecoxib: +543. 151 Da, +545.167 Da; photo-indomethacin: +592.220 Da, +594.236 Da), two missed cleavages and mass tolerance of 10 ppm for the precursor ion, 0.02 Da and 0.6 Da for fragment ions from HCD and C D, respectively. For binding sites of photo- NSAIDs to COX-2 (Table 2), MS data was searched by SEQUEST HT and Byonic against the recombinant COX-2 with the photo-NSAID before and after click chemistry as a modification on any amino acid and assigned to tryptic or semi-tryptic peptides. For the proteomic analysis of K562 and Jurkat cells (Table 3, 4), MS/MS raw files of the tryptic digests were searched against the Swiss-Prot human database (downloaded in 2016) and a contaminant protein database. The statistically significant enriched proteome were determined according to the procedure of Washburn and co-workers. 6 Briefly, the normalized spectral abundance factor (NSAF) was calculated as the number of spectral counts divided by the protein's length, and then divided by the sum of spectral counts for ail proteins in the experiment. The zero NSAF values were replaced by the minimum measured NSAF value and the natural log transformation of NSAF values was used for evaluation with the statistical t-test. Normalized protein assignments at 1% FDR were considered statistically significantly enriched if the fold change was greater than two and the associated p-vaiue was <0.05 (t-test) in labeled samples than in samples treated with the tag 7 . For experiments where biological replicates were not obtained, enrichment was determined by subtraction of all proteins observed in the samples treated with the tag 7 . MS/MS data from cleavage fractions were searched against the entire proteome identified in tryptic digests for direct binding site characterization (Table 5). All calculations were performed in Microsoft Excel and ail peptide spectral matches (PSMs) at 5% FDR were manually validated for precursor isotopic pattern in the MS and spectral assignment in the MS2. Synthetic Procedures [0194] Synthesis of methyl (S )-2-(6-hydroxynaphthalen-2-yl) propanoate (SI) : {1 } e p

[0195] Step / ; Naproxen (1, 5.00 g, 2 1.7 mmol, 1 equiv) was added to aqueous HBr (48% w/w, 35 mL, 309 mmol, 14.2 equiv) in a round bottom flask fitted to a reflux condenser. The reflux condenser was connected to a vented trap containing saturated aqueous sodium bicarbonate solution. The mixture was stirred for 12 hours at reflux. The product mixture was cooled over 30 minutes to 24 °C. The cooled solution was poured in deionized (DI) water (200 mL) and cooled in an ice bath until a visible white precipitate was formed. The precipitate was filtered through a fritted funnel, washed with DI water (3 30 mL) and dried for 2 hours in air.

[0196] Step 2 : The crude white powder was dissolved in methanol (40 mL) Acetyl chloride (2.30 mL, 32.6 mmol, 1.50 equivalents) was added to the resulting solution at 0 °C and the mixture was heated for 4 hours at reflux. The product mixture was cooled over 30 minutes to 24 °C and evaporated to dryness. The resulting material was azeotroped with benzene (2 20 mL) to afford compound SI as an off-white solid (4.70 g, 95%). [0197] r 0.30 (20% ethyl acetate-hexane; UV). NMR (500 MHz, DMSO-de): δ 9.71 (s,

1H, Si;:,). 7.73 (d, .1 7.2 Hz, H2), 7.65-7.63 (m, 2 ¾/¾), 7.3 (d, H, J = 8.0 Hz, 66),

7. 1-7.09 (m, 2H, H1/H3), 3.90 (q, H, J = 7.3 Hz, 1-,).. 3.58 (s, 3H, Hs), 1.46 (d, 3H, J = 7.3

Hz, ! · ). C NMR (125 MHz, DMSO-d ) : δ 174.9 (C), 155.7 (C), 135.2 (C), 134.1 (C), 129.6 (CH), 128.1 CO. 126.8 (CH), 126.4 (CH), 126.1 (CH), 119 3 (CH), 108.9 (CH), 52 2 (OCH ),

44.8 (CH) 18.9 (CH 3). R (ATR-FTIR), cm : 3348 (br), 2982 (m), 2957 (m), 2940 (m), 1703 (s), 1637 (s), 1613 (s), 1509 (s), 1486 (s), 1437 (m), 338 (s), 1208 (m), 1171 (m), 1 47 (m), 927 (m), 857 (m), 808 (m), 558 (m), 471 (m). LRMS-ESI (m/z): [M+H] + calculated for

C14H15O3, 231.1; found, 231.2. [0198] The MR and 1 C NMR of S prepared by the above procedures were in agreement with those reported previously. 7

[0 1 9] Svnthesi of methyl (S)-2-(6-(2-( 3-(but-3 -yn- 1-yl)-3H-di azirin-3 - yl)ethoxy)naphthalen-2-yl)propanoate 2): [0200] Potassium carbonate (300 mg, 2.17 mmol, 2.10 equiv) and iodide S7 (350 mg, 1.40 n mo , 1.00 equiv) was added to a solution of SI (250 mg, 1.04 mmol, 1 equiv) in DMF (6.0 mL). The mixture was stirred for 12 hours at 35 °C. The product mixture was poured into a separator}' funnel containing DI water (15 mL) and diethyl ether (30 mL). The organic portion was separated, washed with brine and dried over magnesium sulfate. The magnesium sulfate was filtered off and the ethereal solution was concentrated in vacuo to afford a waxy material. The material was purified using flash-column chromatography (eluting with 0-40% ethyl acetate-hexane, two steps) to afford the diazirine S2 (310 mg, 85%). [0201] R = 0.37 (20 % ethyl acetate-hexane; UV). ¾ NMR (500 MHz, CDC1 ) : δ 7.74 (d,

H, J = 8.5 Hz, H2), 7.71 (d, 1H, J = 8.2 Hz, H ), 7.68 (s, 1H, H4), 7.43 (dd, 1. J = 8.5, 1.8 Hz, H ), 7.18 (dd, H, J 8.9, 2.5 Hz, Hi), 7.10 (d, . J = 2 4 Hz, H ), 3.97 ( , 2H, J 7 2

Hz, H ), 3.87 (q, , J 7.2 Hz, H9), 3.68 (s, 3H, H ), 2. (td, 2H, J == 8.1, 5.0 Hz, H ), 2.02 (t, IH, J = 5.0 Hz, H i ), 1.98 (t, 2H, J = 7.2 Hz, H ), 1.78 (t, 2H, J = 7.2 Hz, H12), 1.60

(d, 3H, J ==7 1 Hz, · . C NMR (125 MHz, CDCI3); δ 175 1 (C), 156 4 (C), 135.9 (C), 133.6 (C), 129.4 (CH), 129.1 (C), 127.2 (CH), 126.3 (CH), 125.9 (CH), 119.1 (CH), 106.6 (CH),

82 8 , 69 2 (CH), 62.6 (OCH ), 52.1 (OCH3), 45.4 (CH), 32 9 (CH ), 32.7 (CH2), 26 7 1 (CN2), 18.6 (CH 3), 13.3 (CH2) . (ATR-FTIR), cm : 3295 (br), 2922, 2852, 2940, 1705 (s), 1634 (s), 1468 (m), 1510 (w), 1468 (m), 1393 (m), 1209 (m), 1180 (m), 939 (m), 8 11 (m), 640 (m), 475 (m), 1172 [0202] (m), 1147 (m), 930 (m), 857 (m), 808 (m), 560 (m), 490 (m) HRMS-ESI (m/z): i i calculated for C21H23N2O3, 351 1 09; found, 351.1710. [0203] Synthesis of (5)-2-(6-(2-(3 -(but-3 -yn- 1-yl)-3H-diazirin-3 -yl)ethoxy)naphthalen-2- yl)propanoic acid [photo-naproxen (4)]: [0204] Compound S2 (200 mg, 570 µηιοΐ, 1 equiv) was added to a 1M NaOH in methanol (3.0 mL). The mixture was stirred for 4 hours at 24 °C. The product material was concentrated in vacuo. The residue obtained was acidified to pH 2, with KHS0 (lM) and the resulting mixture was added to ethyl acetate. The organic portion was separated, dried over anhydrous sodium sulfate, filtered and concentrated in vacuo to afford photo-naproxen (4) as a waxy solid (190 mg, 98%).

[0205] NMR (500 MHz, CDCI3): δ 7.72 (m, 3H, Η 2/Ή 4/ Η 5), 7.45 (d , . J = 8.2, 1.8 Hz,

H ), 7 . 8 (dd, 1H, J = 8.5, 2.4 Hz, Hi), 7.09 (d, 1H, J = 2.4 Hz, H ), 3.97 (t, 2H, J = 7.0 Hz,

H ), 3.90 (t, . J = 7 Hz, Hg), 2 . 13 (id, 2H, J = 7 9, 2 9 Hz, H 2), 2.02 ( , 1H, J 2.6 Hz,

H13), 1.98 (t, 2 , J = 7.1 Hz, H10), 1.80 (t, 2H, J = 7.5 Hz, !l ). 1.62 (d, 3H, 7.2 Hz, -). C

NMR (125 MHz, ( ' Γ)( Ί ) δ 180 (C), 156 5 (C), 135.2 (C), 133.7 (C), 129.4 (CH), 129. 1

(C), 127.2 (CH), 126.3 (CH), 126.1 (CH), 9 .1 (CH), 106.6 (CH), 82.8 (C), 69.2 (CH), 62.6

(OCH2), 45.2 (CH), 32 9 (CH 2), 32.7 (CH 2), 26.7 (CN 2), 18.2 CH ), 13.3 (CH 2) . IR (ATR- f R ), cm 1: 3295 (br), 2921 (w), 2852 (m), 1703 (s), 1633 (s), 1605 (s), 1468 (m), 1393 (m), 1263 (m), 1208 (m), 1180 (w), 939 (w), 853 (w), 812 (w), 641 (w), 475 (w). HRMS-ESI

+ (m/z): [M+Na] calculated for C20H20N2NaO3, 359.1372, found, 359.1372,

Synthesi s of 4~(5-hydroxy~3 -(trifluoromethyl)- IH-pyrazoi - - )benzenesulfonamide

S4 :

[0207] Ethyl 4, 4, 4-trifluoro-3-oxobutanoate (S3, 2.00 g, 10.9 mo , 1 equiv) and 4- hydrazineylbenzenesulfonamide (2.40 g, 0.9 mmol, 1.00 equiv) were dissolved in ethanol (10 mL) and the resulting mixture was stirred for 12 hours at reflux. The product mixture was cooled for 30 minutes to 24 °C The solvent was evaporated in vacuo and the residue was

poured into D water ( 15 mL). The solution was acidified to pH 2 and a white precipitate formed. The precipitate was filtered through a frit funnel, the precipitate was f tered through a fritted funnel and dried for 2 hours in air to afford the benzenesulfonamide S4 as a slight yellow powder (3.30 g, 99 ) [0208] 'Ή Ν Μ (500 MHz, DMSO-d6): δ 12.86 (s, H, H ), 7.96 (m, 4H, H3/H4), 7.46 (m,

2 ! !.. . 5 97 (s, IH, Hi). C NMR (125 MHz, DMSO-de): δ 154.8 (C), 142.7 (CH), 141.9

(q, 2JCF = 37.2 Hz, C), 140.6 (CH), 127.3 (CH), 122.7 (q, 1JCF = 267.4 Hz, CF3), 122.3 (C), δ 1 86 4 (C). F NMR (375 MHz, DMSO-d 6) : -61.5. R (ATR-FTIR), cm : 3449 (br), 3383 (w), 3280 (w), 2983 (w), 2940 (m), 1703 (s), 1637 (s), 1613 (m), 1589 (m), 1579 (m), 1556 (w), 1535 (m), 1436 (m), 1408 (m), 1208 (ni), 1102 (m), 991 (m), 927 (w), 895 (w), 848 (w), 795 (w), 778 (m), 706 (w), 541 (w), 470 (w)

[0209] Svnthesi s of 4-(5-(2-(3 -(but-3-yn- 1-yl)-3H-diazirin-3 -yl)ethoxy)-3 -(trifluoromethyl)- lH-pyrazol-l-yl)benzenesulfonamide (S):

[0210] A mixture of compound S4 (90.0 mg, 286 µτηοΐ , 1 equiv), and iodo-diazirine S7 (70.0 n g, 286 µιηοί , 1.00 equiv) was dissolved in DMF (3.0 mL) at 24 °C. To this mixture, was added potassium carbonate (40.0 mg, 286 µηιο , 1 00 equiv) and stirred for 12 hours at 24 °C. The reaction mixture was partitioned between ethyl acetate (30 mL) and DI water ( 5 mL) and the organic portion was separated and washed with brine (3 χ 15 mL). The combined organic portion was dried over anhydrous sodium sulfate, filtered and concentrated in vacuo to afford an off white powder. The powder was purified by flash column chromatography (30-60% ethyl acetate-hexane, three steps) to afford photo-celecoxib (5) as a white powder (92.0 mg, 75%). [0211] Rf = 0.20 (40% ethyl acetate-hexane; UV). H NMR (500 MHz, CDCb): δ 8.05 (d,

2H, J = 8.2 Hz, H ), 8.02 (d, 2H, J = 8 1 Hz, H4), 5.95 (s, H, Hi), 5.13 (br, 2H, ! , 4.04 ( , 2H, J = 7.2 Hz, H ), 2.05-2.03 (m, 5H, ¾ ¾ ¾ ), 1.71-1.69 (m, 2H, C NMR (125 MHz, CDCI3): δ 154.6 (C), 143.0 (q, 2JCF = 38.8 Hz, CH), 141.1 (C), 140.4 (C), 127.6 (CH), 22.5 (CH), 121.7 (q, 1JCF = 267 5 Hz CF ), 85.3 (C), 82.4 (C), 69 7 (CH), 67.6 (OCH2), δ 32.4 (CH2), 32. 1 (CH2), 26.1 (CN2), 13.2 (CH 3). F NMR (375 MHz, CDCI3): -63.6. (ATR-FTIR), cn : 3277 (br), 1590 (s), 1563 (m), 1512 (m), 1490 (w), 1416 (m), 1380 (w), 1335 (w), 1246 (m), 151 (m), 1101 (m), 968 (w), 908 (w), 840 (w), 743 (w), 715 (w), 626

(m), 543 (w) HRMS-ESI (m/z): j J i f calculated for C17H17F3N5O3S, 428.0999; found, 428.0949. [0212] Svnthesi s of N-(2-(3 -(but-3 -yn- 1-yl 3H-d aziri n-3 -vPethyl )-2-f 1-(4-chlorobenzovO-

5-methoxy-2-methyl-lH-indol-3-yl)acetamide (6) :

[0213] N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (4 18 nig, 2.19 mmol, .50 equiv), triethyl amine (400 µ , 2.98 mmol, 2.00 equiv), N'~ dimethylaminopyridine (36.0 mg, 290 µτηοΐ , 0.20 equiv) and the amine S6 (200 mg, 1.46 mmol, 1.00 equiv) were added in sequence to a solution of indomethacin (3, 522 mg, 1.46 mmol, 1 equiv) in DMF (10 mL) at 24 ' C . The reaction mixture was stirred for 12 hours at 24

°C and then quenched by addition of potassium hydrogen sulfate (1M, 10 mL). The mixture was transferred into a separately funnel containing ethyl acetate (50 mL). The organic portion was separated, washed with brine (3 10 mL) and the dried over anhydrous sodium sulfate. The sodium sulfate was filtered and the eluent was concentrated in vacuo to afford a crude residue. The crude residue was dissolved in ethyl acetate and crystallized from hexane to afford photo-indomethacin (6) as a white solid (615 mg, 88%). δ [0214] "H R (500 MHz, CDC13) : 7.70 (d, 2H, J = 8.0 Hz, Hn), 7.49 (d, 2H, J = 7.8 Hz, H ), 6.92 (s, 1 ί Hi), 6 9 (d, I I, J = 9.0 Hz, H ), 6 72 (d, 1H, J = 9.0 Hz, ! 5.78 (s, 1

H ), 3 83 (s, 3H, Ho), 3.65 (s, 2H, H4), 3.1 1 (t, 2H, J = 7.2 Hz, ¾), 2.42 (s, 3H, Hio), 1.88

(d l, 2H, J = 7.5, 2.4 Hz, H ), .84-1.83 (m. . H ) 1.62 (t, 2H, t, J = 7.0 !]/, s,,}. 1 53 (t,

2H, J = 7.2 Hz, ). 3C MR (125 MHz, CDC! :): δ 169.9 (C), 168.2 (C), 156.2 (C), 139.4

(C-Cl), 136.4 (C), 133.5 (=C-CH3), 13 1.1 (CH), 130.9 (CH), 130.3 (C), 129 1 (=C-NR2),

115.1 (CH), 112.6 (CH), 12.2 (C), 100.9 (CH), 82.5 (C), 69.3 (CH), 55.7 (OCH 3), 34.6

(CH 2), 32 4 (CH 2), 32. 1 (CH 2), 31.8 (CH), 26.7 (CN 2), 13.3 (CH 2), 12.9 C! ) (ATR- FTIR), cm 1: 3297 (br), 3066 (w), 2930 (w), 2835 (w), 1673 (s), 1650 (m), 1590 (w), 1525 (s), 1476 (m), 1455 (m), 1356 (m), 1314(s), 1222 (s), 1148 (w), 1088 (m), 1065 (w) 909 (w), 833 (w), 728 (w), 644 (w) 481(w). R S- S (m/z): |M !! calculated for , 477.1693; found, 477. 1660. 0215] Synthesis of the photo-glutarimide 8:

[0216] Step 1. Synthesis of 2-(3-(but-3-yn-l-yl)-3H-diazirin-3-yl)ethyl lH-imidazole-1- earboxyiate (S5): To a solution of 2-(3-(but-3-yn-l-yl)-3H-diazirin-3-yl) ethan-l-ol (200 mg, 1.45 mmol, 1 equiv) in tetrahydrofuran (10 ml.) at 24 °C, was added carbonyldiimidazole

(950 mg, 5 80 ol, 4.00 equiv). The mixture was allowed to stir for 12 hours at 24 °C. The product mixture was concentrated in vacuo to a solid residue. The residue was directly loaded to a hexane-equiiibrated silica gel column and the desired material was eluted using a 50- 100% ethyl acetate-hexane solvent, two steps). The imidazole S5 was isolated as colorless oil after concentration of the residual solvent (320 mg, 95 ) δ [0217] Rf = 0.15 (40% ethyl acetate-hexane: UV). ¾ NMR (500 MHz, CDC1 ) : 8.13 (s, 1 He) 7.42-7.41 (m, 1H, H ), 7.03-7.02 (m, H, Hg), 4.26-4.23 ( , 2H, J 7 1 Hz, ¾),

1.99-1.96 , 3H, ¾/¾), 1.91-1.88 (t, 2 , J = 6.9 Hz, ¾), 1.66-1.63 (t, 2 , J = 7.1 Hz,

¾). C NMR (125 MHz, CDC1 ) : δ 148.3 (C), 137.1 (CH), 130 7 (CH), 117.1 (CH), 82 3

( , 69.6 (CH), 62.9 (OCH 2), 32. 1 (CH?), 32.0 (CH2), 26.0 (CN2), 13.1 (CH2) . R (ATR- FTIR), cm 1: 3291 (br), 3 158 (w), 3132 (m), 2960 (w), 2921 (m), 2858 (m), 1758 (s), 1588 (s), 1525 (m), 1473 (m), 1444 (m), 1404 (m), 1380 (w), 1316 (w), 1282 (w), 1240 (w), 1173 (w), 1095 (m), 1058 (m), 1003 (w), 898 (m), 833 (w), 768 (w), 749 (w), 649 (w), 598 (w),

526 (w). HRMSESI (m/z): [M+H] + calculated for C 11H13N4O2, 233.1039; found, 233.1064.

[0218] Step 2. Synthesis of 2-(3-(but-3-yn-l-yl)-3H-diazirin-3-yl)ethyl (2,6-dioxopiperidin- 3-yl)carbamate (8): l,8-Diazabicyclo[5.4.0]undec-7-ene (650 mg, 4.31 mmol, 5.30 equiv) and 3-aminopiperidine-2,6-dione hydrochloride (600 mg, 2.58 mmol, 3 14 equiv) were added in sequence to a stirred solution of 2-(3-(but-3-yn-l-yl)-3H-diazirin-3-yl)ethyl lH-imidazole- 1-carboxylate (200 mg, 820 umol, 1 equiv) in DMF (10 mL). The mixture was stirred for 12 hours at 24 °C. The product mixture was partitioned between ethyl acetate (30 .) and DI water (20 mL). The organic portion was separated and the aqueous portion was extracted with ethyl acetate (2 20 mL). The combined organic portion was washed with D water (4 10 mL) then with brine ( 0 mL). The solution was dried over anhydrous sodium sulfate, filtered and concentrated in vacuo to afford the c de material. The crude was purified by silica gel flash chromatography (using 20-60% ethyl acetate-hexanes, two steps) to afford the photo-glutarimide 8 as an oil (220 mg, 86%). [0219] 0.20 (40 % ethyl acetate-hex ane). ¾ NMR (500 MHz, CDCI3): δ 8.60 (m, H,

H10), 5.72 (m, H, He), 4.41-4.36 m, H, H7), 4.02 (t, 2H, J = 5.7 Hz, ¾), 2.84-2.49 m, 4H, Η Η ¾/¾), 2 04- 1.91 (m, 3H, 2/ ), 1.78 (t, 2H, J = 6.2 Hz, H4), 1.70 (t, 2H, J = 7.2 Hz, H 3) . C NMR (125 MHz, CDCI3): δ 171.6 (C), 171.4 (C), 155.9 (C), 82.6 (C), 69.4 (CH), 65.1

(CH), 60.2 (OCH2), 32.5 (CH 2), 32 2 (CH 2), 31.2 (CH 2), 25.2 (CN 2), 13.2 (C !·) (ATR- FTIR), cm 1: 3283 (br), 3 07 (w), 2958 (w), 291 8 (m), 2858 (w), 1694 (s), 1587 (s), 1527 (m), 1356 (nil 133 1 (m), 1302 (m), 1 97 (m), 1082 (w), 1063 (m), 1037 (m), 991 (w), 776 (m), 650 (m), 472 (m). HRMS-ESI (m/z): [M+Na] + calculated for \ a i. 315.1069; found, 315.1076.

0220] Synthesis of l-phenyl-3-(trifluoromethyl)-lH-pyrazol-5-ol (S9) :

S3 92%

[0221] Ethyl 4, 4, 4-trifluoro-3 -oxobutanoate (S3, 200 _uL, 1.37 mmol, 1 equiv) and phenylhydrazine (148 µ , 1.37 mmol, 1.00 equiv) were dissolved in ethanol (1.4 mL) and the resulting mixture was stirred for 12 hours at reflux. The reaction mixture was cooled to 24 ' C and the solvent was evaporated in vacuo. The residue was dissolved into ethyl acetate (3 mL) and washed with IN HC1 (3 3 mL). The organic layer was dried over sodium sulfate, filtrated and concentrated in vacuo. The resulting material was washed with dichloromethane (5 mL) to afford the compound as orange solid (289 mg, 92%).

[0222] R s 0.25 (30% ethyl acetate-hexanes, UV). ¾ NMR (500 MHz, DMSO-d&): δ 7.71

(d, 2Ή , H2, J = 8.0 Hz), 7.5 (dd, 2H, J = 8.0 Hz, H 3), 7.38 (t, IH, J = 8.0 Hz, H4), 5.94 (s,

IH, Hi). C NMR (125 MHz, DMSO-de): δ 153.7 (C), 140.4 (q, 2JCF = = 37.4 Hz, C), 137.7 (C), 129.1 (CH), 127.2 (CH), 122.3 (CH), 121.3 (q, 1JCF = 266.9 Hz, CF ), 85.6 (q, 3JCF = 1.6 Hz, CH). F NMR (375 MHz, DMSO-de): δ -61.8. R (ATR-FTIR), cm 1: 3373 (br),

1599 (rn), 1505 (m), 1491 (m), 1456 (m), 1407 (m), 1151 (s), 1119 (s), 984 (s), 758 (s), 691 (s). HRMS-ESI (m/z): [M+H] + calculated for Ci H F N O, 229.0583; found, 229.0598.

[0223] Synth esi s of 5~(2-f3-(but-3 -yrs- 1-y1)-3 H-diazi ri n-3 -y )eth ox )- 1-ph e -3- (trifluorom ethyl)- lH-pyrazole (9) :

mm

[0224] A mixture of compound S9 (38.1 mg, 167 µτηοΐ , 1 equiv) and iodo-diazirine S7 (41.4 mg, 178 µτηοΐ , 1.00 equiv) was dissolved in DMF (1.7 mL) at 24 °C. Potassium carbonate

(46.1 mg, 334 µτηοΐ , 2.00 equiv) was added to the resulting mixture. The reaction mixture was stirred for 12 hours at 50 °C, then cooled for 30 minutes to 24 °C and partitioned between ethyl acetate (5 mL) and DI water (5 mL). The organic portion was separated and washed with brine (3 5 mL). The organic portion was dried over anhydrous sodium sulfate, filtered and concentrated in vacuo to afford an off white powder. The powder was purified by flash column chromatography (20% ethyl acetate-hexanes) to afford the celecoxib analog 9 as a pale yellow oil (39.4 mg, 68%). [0225] R = 0.58 (20% ethyl acetate-hexanes: UV). HNMR (500 MHz, CDCh): δ 7.74 (d, 2H, J = 7.6 Hz, ), 7.48 (dd, 2H, J = 7 6, 7 6 Hz, H ), 7.36 (t, 1H, J 7 6, 7.6 Hz, ¾), 5.92

(s, 1H, Hi), 3.99 (t, 2H, J = 6.0 Hz, H2), 2.01-1.95 (m, 5H, ¾/¾/¾), 1.66 (t, 2H, J = 6.8 Hz, δ I-) C NMR. (125 MHz, CDC13) : 154.0 (C), 141.8 (q, 2JCF = 38.4 Hz, CH), 137.5 (C), 129.0 (CH), 127.7 (CH), 123.0 (CH), 120.9 (q, 1JCF = 267.3 Hz CF ), 84.7 (q, 3JCF = 2.1

Hz, CH), 82.4 (( .. 69.4 (CH), 67. 1 (OCH 2), 32.6 (C ! }.. 32.3 (CH 2), 26. 1 (CN ), 13.2 (CH ). F NMR (375 MHz, CDCh): δ -63.3 ppm 01 (ATR-FTIR), cm- 1: 3303 (s), 1594 (m), 562 (m), 1508 (m), 1488 (m), 1457 (m), 1243 (s), 26 (s), 1099 (s), 968 (s), 759 (s), 639 (s) cm-

1. HRMS-ESI (m/z): ( ! calculated for C17H16F3N4O, 349.1271 found, 349 1276

[0226] Synthesis of 2-aminoethyl 2-azidoacetate (S ): S1S S 98%

[0227] Step 1. Acid chloride formation: Azidoacetic acid (S10, 154 mg, 1.49 mmol, 1 equiv) was dissolved i methanol (10 mL) at 24 °C. Acetyl chloride ( 1 L, 2.49 mmol, 2.00 equiv) was added dropwise to the stirred solution at 24 °C. The resulting mixture was stirred for 6 hours at 24 °C. The product mixture was evaporated to dryness and used directly in the following step.

[0228] Step 2. Synthesis of 2-aminoethyl 2-azidoacetate (Sll): The azido-acetyl ch ori e (151 mg, 1.49 mmol, 1 equiv) obtained in the previous step was dissolved in methanol (10 mL) at 24 °C. Aminoethanol (450 _uL, 7 47 mmol, 5.00 equiv) was added dropwise to the stirred solution at 24 °C. The resulting mixture was stirred for 16 hours at 24 °C. The product mixture was concentrated to dryness. The residue obtained was purified by flash-column chromatography (eluting with 10% ethyl acetate-hexanes, grading to 20% ethyl acetate- hexanes, one step) to afford 2-aminoethyl 2-azidoacetate (Sll) as clear yellow oil (209 mg, 98%). [0229] R = 0.60 (10% methanol-dichloromethane; ninhydrin). ¾ MR (500 Hz, CDCh): δ

7 0 1 (br s, III, Hi), 3.96 (s, 2H, ¾), 3 68 (t, 2H, J = 5.0 Hz, H ), 3 57 (br s, III, H4), 3.41 (td, δ 2H, J = 5.5, 5.0 Hz, H2). C MR (125 Hz, CDCh): 167.7 (C), 62.0 (CH 2), 52.8 (CH 2), - 1 42.3 (CH 2) . R (ATR-FTIR), cm : 3306 (s), 2107 (s), 1655 (s), 1548 (m). HRMS-ESI (m/z): [ l ] calculated for C4H9N4O2, 145.0726; found, 145.0720.

102301 Synthesis of 2-aminoethyl 2-azidoacetate CS13 :

[0231] Step 1. Acid chloride formation: Azidoacetic acid~13C2 (S12, 146 mg, 1 42 mmol, 1 equiv) was dissolved in methanol (10 mL) at 24 °C. Acetyl chloride (200 uL, 2.84 mmol, 2 00 equiv) was added dropwise to the stirred solution at 24 °C. The resulting mixture was stirred for 6 hours at 24 °C. The product mixture was evaporated to dryness and used directly in the following step.

[0232] Step 2. Synthesis of 2-aminoethyl 2-azidoacetate (S13): The azidoacetyi chloride- C2 (172 mg, 1.42 mmol, 1 equiv) obtained in the previous step was dissolved in methanol (10 mL) at 24 °C. Aminoethanol (427 µ , 7.10 mmol, 5.00 equiv) was added dropwise to the stirred solution at 24 °C. The resulting mixture was stirred for 16 hours at 24 °C. The product mixture was concentrated to dryness. The residue obtained was purified by flash-column chromatography (eluting with 10% ethyl acetate-hexanes, grading to 20% ethyl acetate- hexanes, one step) to afford 2-aminoethyl 2-azidoacetate- C (S13) as clear yellow oil (207 mg, 99%).

[0233] R s 0.60 (10% methanol-dichloromethane; ninhydrin). ¾ NMR (500 MHz, CDC1 ) : δ 6.73 (br s, 1H, Hi), 4.17-3.87 (dd, 2 , JCH = 144.1, 5.8 Hz, H5), 3.76 (t, 2H, J = 5.5 Hz, δ ¾), 3.48 (id, 2 1 J = 5.5, 2 0 Hz, H2), 2.30 (br s, H I, ) C NMR (125 MHz, CDCb):

167.7 (d, JCC = 54.9 Hz, 13C), 62.1 (CH ), 52.9 (d, JCC = 54.9 Hz, 13CH2), 42.3 (CH2). (ATR-FTIR), cm 1: 3272 (s), 2946 (s), 2017 (s), 1654 (s). HRMS-ESI (m/z): [M+H]+ calculated for C 2 C2 9 0 2, 147 0793; found, 147.0789.

0234] Synthesis of the cleavable biotin azide probe 10:

[0235] Triethylamine (102 L, 736 µηιο , 20.0 equiv) and dichiorodiphenyisiiane (38.8 uL, 184 µ ηο , 5.00 equiv) were added in sequence to a stirred solution of the biotin-CA(PEG) - alcohol S145 (20 7 mg, 36.8 µη ο , 1 equiv) i dichlorom ethane (370 µΐ ). The resulting solution was stirred for 2 hours at 24 °C. A 1:3 mixture of the azide Sll and the azide- C2 S13 (53.0 mg, 368 µηιο , 10 0 equiv) was added to the stirred solution. The resulting solution was stirred for an additional 12 hours at 24 °C. The product mixture was diluted sequentially with dichloromethane (3 mL) and saturated aqueous sodium bicarbonate solution (3 mL). The resulting biphasic mixture was transferred to a separator}' funnel and the layers that formed were separated. The aqueous layer was extracted with dichloromethane (3 · 3 mL), and the organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered, and the filtrate was concentrated by rotary evaporation. The residue obtained was purified by flash-column chromatography (eluting with 1% methanol- dichloromethane, grading to 10% methanol-dichloromethane, 3 steps) to afford the IsoTaG azido silane probe 10 as a clear oil ( 6.6 mg, 51%). δ [0236] Rf = 0.43 (5% methanol-dichloromethane: 12). N.MR (600 MHz, CD3OD): 7.66 (d, 4 1 J = 6.6 Hz, H ), 7.43 (t, 2 1 J = 7.2 Hz, 1h ), 7.37 (t, 4H, J = 7.8 Hz, H ), 4.47 (dd,

H, J = 7.8, 5.4 Hz, H2), 4.29 (dd, H, J = 7.8, 4.2 Hz, H ), 3.94 (d, 0.5H, J = 4.8 Hz, H2 ),

2 1 H13), Η Η Η 3 85- 3 83 (m, 1.5H, H2 ), 3.71 (t J = 6.0 Hz, 3.61- 3 55 (m, 18H, / 2 ), H22), 3.52 (t, 2H, J = 6.5 Hz, H2 ), 3.44-3.41 (m, 0.5H, 3.35 (t, 1.5H, J = 5.0 Hz, H22), 3.19 (dt, i l J 5.0, 4.5 Hz, H ), 2.92 (dd, H, J = 12.6, 5.4 Hz, Hi), 2.69 (d, H, J 12 6 Hz,

Hi), 2.45 (t, 2Ή , J = 6.0 Hz, H ), 2.21 (t, 2Ή , J = 7.5 Hz, H 0), 1.75-1.55 (m, 4H, H7/H9),

1 44 (quint, 2H, J 7.5 Hz, ¾), 1.25 (s, 6H, Η & Η ). C NMR (151 MHz, CD3OD): δ 176.1 (C), 174.1 (C), 170.2 (d, JCC = 52.8 Hz, 13C), 166.1 (C), 136.1 (4 χ CH), 135.6 (2 χ

χ χ C), 131.4 (2 y CH), 128.9 (4 CH), 77.0 (CH 2), 71.6 (CH 2), 71.5 (3 x CH ) 71.3 (2 CH2),

70.6 (CH 2), 68 4 (CH 2), 63.4 (CH), 62 7 (CH 2) 61 6 (CH), 57.0 (CH 2), 52 97 (d, Jcc = 52.8

Hz, CH2,), 5 .6 (CH 2), 42.6 (CH 2), .1 (CH 2), 40.4 (CH 2), 37.8 (CH ), 36.7 (CH 2), 29.8 χ (CH 2), 29 5 (CH 2), 28 2 (2 CH ), 26 8 (CH ) 0 (ATR-FTIR), cm : 3296 (br), 2927 (m), 2103 (s), 1683 (s), 1644 (s), 1 6 (s). HRMS-ESI (m/z): [M+Na] ÷ calculated for

!H& C4 2N80ioSSiNa/C39 C2H62N80ioSSiNa, 909.3977/91 1.4044; found, 909 3932/9 1.3986.

Additional References for Methods (1) Still, W. C ; Kahn, M.; Mitra, A . J . Org. Chem. 1978, 43, 2923. (2) Pangborn, A . B ; Giardello, M A., Grubbs, R . H , Rosen, R . K.; Timmers, F . J Organometallics 1996, 15, 1518. (3) Lee, P . J . J.; Compton, B . J.; Patent, U . S., Ed.; Waters Investments Limited: USA, 2007; Vol. 7229539. (4) Wang, W.; Hong, S.; Tran, A.; Jiang, H.; Triano, R.; Liu, Y.; Chen, X ; Wu, P . Chem Asian J

201 , 6, 2796. (5) Szychowski, J.; Mahdavi, A.; Hodas, J . J L , Bagert, J . D.; Ngo, J T.; Landgraf, P.; Dieterich, D . C ; Schuman, E . M.; Tirrell, D . A . J . Am. Chem Soc. 2010, 132, 18351. (6) Zybailov, B , Mosley, A . L.; Sardiu, M E., Coleman, M . K.; Florens, L.; Washburn, M . P . J Proteome Res 2006, 5, 2339. (7) Mesangeau, , Peres, B.; Descamps-Francois, ; Chavatte, P.; Audinot, V.; Coumailleau, S.; Boutin, J . A.; Delagrange, P.; Bennejean, C ; Renard, P.; Caignard, D . H.;

Berthelot P.; Yous, S. Bioorg Med Chern 2010, 18, 3426.

Example 2: Synthesis of an electronically-timed minimally interfering alkynylphoto-affinity label to measure small molecule protein interactions [0237] Reported herein is the synthesis of an electronically-tuned minimally interfering photoaffinity label (MI-PAL), a compact five-carbon tag functionalized with an alkyl diazirine and alkyne handle. MI-PAL is compatible with protein photo-conjugation, click chemistry and mass spectrometry and readily installed to complex molecules for biological target identification. [0238] The development of small multifunctional chemical tags that are readily embedded to a small molecule has accelerated target identification for non-covalent iigands. These chemical tags typically possess two primary functions: first, photo-conjugation chemistry to covalently capture the protein target and second, a reporter group for characterization of the liganded proteome. 1,2 Photo-affinity labels (PALs) like the aryl azide, benzophenone, and diazirine generate short-lived highly reactive nitrene, carbene or diradical intermediates, respectively, that insert to nearby biomolecules. 5 The covalent conjugation event facilitates subsequent iigand-dependent detection of the biomolecule. To allow for the greatest flexibility in detection, a biocompatible handle (e.g., alkyne) is commonly embedded to the chemical tag for versatile functionalization with a reporter molecule via copper-catalyzed azide-alkyne cycloaddition (CuAAC). 4 [0239] Equally important is the facile integration of the chemical tag to the ligand in a minimally perturbative manner in order to preserve the native interactions of the ligand with the proteome. Thus, of the available PALs, the diazirine has seen recent application in numerous target identification studies due to its small size. 8 Integration of the diazirine with an alkyne reporter handle have yielded chemical tags like the aryl diazirine I ,9 10.1 A in length, or the "minimalist" tag (2), 9.4 A in lengt (Figure 28). The minimalist tag (2) has been applied to drug on-target and off-target identification, 12,11 fragment based screening, 13 and binding site mapping. 14,13 [0240] Synthesis of an electronically-tuned five carbon tag, such as the diazirine 3, would afford a smaller alkyl tag scaffold (6.9 A) 1 with universally improved photoconj ugation and CuAAC properties (Figure 28). Photochemical carbene intermediates and CuAAC reaction kinetics are strongly dependent on electronic substituent effects. Electronic stabilization of the reactive carbene by fluorine was first demonstrated with 3-trifluoromethyl-3- phenyldiazirine, which possessed superior stability and selectivity as compared to aiky diazirines. 16 Reactive carbenes formed from diazirines can produce intramolecular and intermolecular products that may differ based on the substituents adjacent to the carbene. 5 Electronic tuning of the aikyne with fluorine likewise accelerates strain-promoted azide- alkyne cycloaddition 7 and CuAAC, with measured improvements in reaction rates of 18-fold greater for the difluoropropyne relative to the dihydropropyne. 18 Based on these data, we hypothesized that strategic placement of fluorine adjacent to the aikyne and diazirine functional groups would improve the essential properties required for the chemical tag and provide synthetic access to a minimally-interfering photo-affinity label (MI-PAL, 3). The tag was retrosynthetically accessed by coupling the ester 4 to a monobromodifluoroalkyne 5, followed by installation of the diazirine. [0241] Synthesis of MI-PAL (3) commenced from the ester 4 and the monobromodifluoroalkyne 5 {Figure 29). The nucleophiiic addition of the monobromodifluoroalkyne 5 to the alphahydroxyethyl ester 4 afforded the desired difluoroketone 6 and the hydrate 7 in 77% yield as a 1: mixture. The hydrate 7 was formed in situ due to the electrophilicity of the difluoropropyne. A brief investigation of the scope of the initial coupling step revealed that the desired reaction was promoted by the methoxymethyl ester forming a lithium chelate complex preventing collapse to the ketone at low temperatures. The equimolar mixture of ketone 6 and hydrate 7 was then treated with hydroxy! amine, followed by a sequence of tosyl chloride in pyridine and ammonia in ether to install the diaziridine 8 . Elaboration of the ketone 6 to the diaziridine 8 was enabled by the difluoropropyne protected with triisopropylsilane (TIPS) to prevent undesired nucleophiiic or deprotonation pathways promoted by basic ammonia. Oxidation (iodine, trimethylamine) of the diaziridine 8 afforded the diazirine 9 in 65% overall yield from the mixture of 6 and 7 . Acid deprotection (TMSC1, MeOH) of the diazirine 9 revealed the alcohol 10 (99%). The alcohol 10 could be further desilylated to yield MI-PAL (3) itself (66%). However, we found that MI-PAL (3) was relatively volatile (boiling point =86 °C) and thus in practice rarely- removed the TIPS protecting group until after incorporation of MI-PAL (3) to a small molecule of interest. The advanced alcohol intermediate 10 was thus prepared by a four-step sequence in high overall yields (49% overall). [0242] With MI-PAL (3) in hand, we next evaluated the photochemical and CuAAC properties bybmass spectrometry and Western blot. MI-PAL (3, 10 µΜ ) was incubated with an isolated protein, alpha-crystal lin, and photo-irradiated (365 nm) for 5 minutes (Figure 3OA). The conjugated protein was trypsin digested and analyzed by liquid chromatography- tandem mass spectrometry on an Orbitrap Elite by collision induced dissociation (CID). Tandem mass spectra of MI-PAL (3) conjugated-peptides obtained by CID displayed characteristic a ky fluorine io losses as diagnostic markers. 19 An example peptide conjugated to MI-PAL (3) is shown in Figure SOB. To test both photo-conjugation and

CuAAC properties, 00 µΜ of MI-PAL (3) was incubated with MM. S or K562 whole cell lysates and photo-irradiated (30 minutes). The MI-PAL photo-conjugated lysates were treated by CuAAC with biotin-azide as a reporter and visualized by Western blot. A UV-specific signal due to biotinylation from samples photo-conjugated to MIPAL (3) was observed (Figure 30C).

[0243] MI-PAL (3) was readily incorporated to a range of small molecules (Figures 31 and 32). The alcohol 10 was activated with carbonyldiimidazole (CDI) in quantitative yield to afford the carbamate 1 (Figure 31). The carbamate 11 was treated with several coupling partners of increasing complexity followed by removal of the TIPS protecting group to reveal the terminal alkyne. The MI-PAL-tagged glycine methylester was formed in 69% yield over two steps. Daunorubicin was readily modified by the carbamate 11 to afford the MI- PAL-tagged daunorubicin 13 i 53% yield over two steps. The alcohol 10 was additionally activated with 4-nitrophenyl chloroformate and installed to mitomycin to prepare the tagged mitomycin analog 14. In all cases, desilylation with TBAF proceeded smoothly following conjugation of MI-PAL to a small molecule. Mitomycin and the MI-PAL-tagged mitomycin

14 displayed similar anti-proliferative activity against 562 cells (ECso = 34 9 µΜ and 40.6 µΜ, respectively).

[0244] We additionally tested the participation of MI-PAL in direct SN2 displacement to modify small molecule ligands (Figure 32). The alcohol 10 was transformed to the iodide 15 in the presence of iodine and triphenylphosphine in excellent yield (99%). The iodide 15 was then elaborated to the naproxen analog 16 in the presence of cesium carbonate in N,N- dimethylformamide. In situ deprotection of the alkyne by cesium carbonate afforded the MI- PAL-tagged naproxen analog 17 in 81% yield. Mixtures of the iodide 15 and cesium carbonate with β-estradioi (18) additionally provided the MI-PAL-tagged β-estradiol 19 in 74% yield. Thus, MI-PAL is readily functionalized to a range of complex ligands to accelerate target identification. [0245] Characterization of the small molecule interactome is dramatically accelerated by chemical tags that enable measurement of the non-covaient interaction between the ligand and its biomolecular targets. Integration of photo-activatable functional groups with a handle for CuAAC in a short chemical tag is arguably the most likely to preserve the native interactions of the small molecule with the protein targets, although the design of a reporter for a small molecule will be structure-dependent. Functional assays to compare the modified small molecule to the parent compound are necessary to validate the preservation of biological activity, including phenotype assays (e.g., cell viability) or in vitro binding assays if the target is known (e.g., fluorescence polarization, SPR, or ITC). Reported herein is the development of an electronically-tuned five carbon tag 3 as a novel minimally-interfering photo-affinity label. M PAL (3) possesses a diazirine appended directly to a difluoropropyne that enables facile synthetic access to the tag and its essential functions in photo-conjugation and CuAAC. We demonstrated the photo-conjugation with a single protein and whole proteome, UV-dependent CuAAC with a biotin-azide reporter, and measurement by mass spectrometry, as well as incorporation of MI-PAL (3) into several complex small molecules. MI-PAL (3) thus constitutes a small electronically-tuned a ky diazirine alkyne tag for application in non-covalent ligand target identification studies.

References

1. Flaxman, H . A.; Woo, C . Biochemistry 2017 2 . Ziegler, S.; Pries, V.; Hedberg, C ; Waidmann, H . Angew Chem Int Ed 2013, 52, 2744- 2792. 3 . Hatanaka, Y. Chem Phartn Bull (Tokyo) 2015, 63, 1-12.

4 . Mackinnon, A . L.; Taunton, J . Curr Protoc Chem Biol 2009, 1, 55-73.

5. Korneev, S. M . Eur J Org Chem 201 1, 201 , 6 153-6175.

6 . Das, J . Chem Rev 2011, 111, 4405- 7

7. Dubinsky, L , Krom, B . P.; Meijler, M . M . Bioorg Med Chem 2012, 20, 554-70 8. Moss, R A . Acc Chem Res 2006, 39, 267-272. 9 Kumar, N S.; Young, R N . Bioorg Med Chem 2009, 17, 5388-95

10. Li, .; Hao, P.; Li, ..: Tan, C . Y. .).: Cheng, X.; Chen, G . Y. J.; Sze, S. K.; Shen, H.-M.;

Yao, S . Q . Angew Chem Int Ed 2013, 52, 8551-8556.

. Su, Y ; Pan, S.; Li, Li, I..; Wu, X.; Hao, P.; Sze, S. K.; Yao, S. Q . Sci Rep 2015, 5, 7724.

12. Pan, S.; Jang, S.-Y.; Wang, D.; Liew, S. S.; Li, Z.; Lee, J.-S.; Yao, S. Q . Angew Chem 2017, 129, 1978-1 983 13. Parker, C . G.; Galmozzi, A.; Wang, Y.; Correia, B . E.; Sasaki, K.; Joslyn, C . M.; Kim, A .

S.; Cavallaro, C . L.; Lawrence, R. M.; Johnson, S R.; Narvaiza, I ; Saez, E.; Cravatt, B. F. Cell 2017, 168, 527-54 l.e29. 14. Gao, J.; Mfuh, A.; Amako, Y.; Woo, C . M . Manuscript under review 2018. 15. The longest linear distance were measured in Gaussian 16 from structures minimized with the Hartree Fock basis set 6-3 lg(d).

16. Brunner, J., Se , H., Richards, F. M . J Biol Chem 1980, 255, 3313-3318

17. Baskin, J . M.; Prescher, J . A.; Laughlin, S. T.; Agard, N . J.; Chang, P. V.; Miller, I. A.; Lo, A.; Codelli, J . A.; Bertozzi, C . R Proc Natl Acad Sci 2007, 104, 16793-16797

18. Gree, D.; Gree, R . Tet Lett 2010, 5 1, 2218-2221.

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EQUIVALENTS AND SCOPE [0246] All publications, patents, patent applications, publication, and database entries (e.g., sequence database entries) mentioned herein, e.g., in the Background, Summary, Detailed Description, Examples, and/or References sections, are hereby incorporated by reference in their entirety as if each individual publication, patent, patent application, publication, and database entry was specifically and individually incorporated herein by reference. In case of conflict, the present application, including any definitions herein, will control. [0247] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents of the embodiments described herein. The scope of the present disclosure is not intended to be limited to the above description, but rather is as set forth in the appended claims. [0248] Articles such as "a," "an," and "the" may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include "or" between two or more members of a group are considered satisfied if one, more than one, or ail of the group members are present, unless indicated to the contrary or otherwise evident from the context. The disclosure of a group that includes "or" between two or more group members provides embodiments in which exactly one member of the group is present, embodiments in which more than one members of the group are present, and embodiments in which all of the group members are present. For purposes of brevity those embodiments have not been individually spelled out herein, but it will be understood that each of these embodiments is provided herein and may be specifically claimed or disclaimed. [0249] It is to be understood that the invention encompasses all variations, combinations, and permutations in which one or more limitation, element, clause, or descriptive term, from one or more of the claims or from one or more relevant portion of the description, is introduced into another claim . For example, a claim that is dependent on another claim can be modified to include one or more of the limitations found in any other claim that is dependent on the same base claim. Furthermore, where the claims recite a composition, it is to be understood that methods of making or using the composition according to any of the methods of making or using disclosed herein or according to methods known in the art, if any, are included, unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise. [0250] Where elements are presented as lists, e.g., in Markush group format, it is to be understood that every possible subgroup of the elements is also disclosed, and that any element or subgroup of elements can be removed from the group. It is also noted that the term "comprising" is intended to be open and permits the inclusion of additional elements or steps. It should be understood that, in general, where an embodiment, product, or method is referred to as comprising particular elements, features, or steps, embodiments, products, or methods that consist, or consist essentially of, such elements, features, or steps, are provided as well. For purposes of brevity those embodiments have not been individually spelled out herein, but it will be understood that each of these embodiments s provided herein and may be specifically claimed or disclaimed. [0251] Where ranges are given, endpoints are included. Furthermore, it is to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value within the stated ranges in some embodiments, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise. For purposes of brevity, the values in each range have not been individually spelled out herein, but it will be understood that each of these values is provided herein and may be specifically claimed or disclaimed. It is also to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values expressed as ranges can assume any subrange within the given range, wherein the endpoints of the subrange are expressed to the same degree of accuracy as the tenth of the unit of the lower limit of the range. [0252] In addition, i is to be understood that any particular embodiment of the present invention may be explicitly excluded from any one or more of the claims. Where ranges are given, any value within the range may explicitly he excluded from any one or more of the claims. Any embodiment, element, feature, application, or aspect of the compositions and/or methods of the invention, can be excluded from any one or more claims. For purposes of brevity, all of the embodiments in which one or more elements, features, purposes, or aspects is excluded are not set forth explicitly herein. [0253] Section headings used herein are not to be construed as limiting in any way. It is expressly contemplated that subject matter presented under any section heading may be applicable to any aspect or embodiment described herein. CLAIMS

What s claimed is:

A photo-click tag comprising (a) a diazirine moiety, and (b) a click chemistry handle.

2. The photo-click tag of claim 1, wherein the diazirine moiety comprises the structure:

3. The photo-click tag of claim or 2, wherein the click chemistry handle is an alkyne.

4 The compound of any one of claim s 1-3, wherein the photo-click tag is of the formula:

5. The photo-click tag of any o e of claims 1-4, wherein the photo-click tag optionally comprises one or more electronegative atoms.

6 . The photo-click tag of claim 5, wherein one or more of the electronegative atoms is fluorine.

7 The photo-click tag of any one of claims 1-6, wherein the diazirine moiety forms a reactive carbene species upon irradiation with a specific wavelength of light. 8. The photo-click tag of claim 7, wherein the specific wavelength of light is between about 0 ran and about 400 nm.

9 The photo-click tag of claim 8, wherein the specific wavelength of light is between about 355 nm to about 365 nm.

10 . The photo-click tag of any o e of claims 7-9, wherein the reactive carbene species reacts with a C-C, C-H, N-H, or O-H bond of a protein.

. The photo-click tag of claim 10, wherein a new covalent bond is formed between the photo-click tag and the protein

12. The photo-click tag of any one of claims 1-1 1, wherein the photo-click tag is between 6 and 9.5 in length.

13. A compound comprising the structure of Formula (I):

wherein S is a small molecule, or derivative thereof; P is a photo-click tag comprising (a) a diazirine moiety and (b) a click chemistry handle; and L is a linker.

14. The compound of claim 13, wherein L comprises an ester, an ether, an amine, or an amide.

15. The compound of claim 13 or 14, wherein L is:

16. The compound of any one of claims 13-15, wherein P is: 17 The compound of any one of claims 13-16, wherein S is an antibiotic, an anti proliferative agent, an anti-cancer agent, a chemotherapeutic agent, an anti-angiogenesis agent, an anti-inflammatory agent, an immunosuppressant, an immunomodulatory agent, an anti-bacterial agent, an anti-viral agent, a cardiovascular agent, a cholesterol-lowering agent, an anti-diabetic agent, an anti-allergic agent, a contraceptive agent, or a pain-relieving agent

18. The compound of claim 17, wherein S is an anti-inflammatory agent, or derivative thereof

19 The compound of claim 18, wherein the a i- f am atory agent is a nonsteroidal anti-inflammatory drug (NSATD), or derivative thereof.

20. The compound of claim 9, wherein the NSATD is naproxen, celecoxib, indomethacin, or derivative thereof.

2 1. The compound of claim 1 or 20, wherei n the compound is of the formula: or a pharmaceutically acceptable salt thereof.

22. The compound of claim 17, wherein S is an immunomodulatory drug, or derivative thereof.

23. The compound of claim 22, wherein the immunomodulator) ' daig is thalidomide, lenalidomide, pomalidomide, or derivative thereof.

24. The compound of claim 23, wherein the lenalidomide is R-ienalidomide.

25. The compound of claim 23, wherein the lenalidomide is S-lenalidomide.

26. The compound of any one of claims 22-25, wherein the compound is of the formula: a pharmaceutically acceptable salt thereof. 503 28. The compound of claim 17, wherein S is a chemotherapeutic agent, or derivativ* thereof

29 The compound of claim 28, wherein the chemotherapeutic agent is mitomyosin, daunorubicin, or derivative thereof

30. The compound of claim 28 or 29, wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof. 31. The compound of any one of claims 13-16, wherein S is a steroid, or a derivative thereof.

32. The compound of claim 31, wherein the steroid is an estrogen, or a derivative thereof.

33. The compound of claim 32, wherein the estrogen is beta-estradiol, or a derivative thereof.

34. The compound of any one of claims 3 -33, wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof.

35. The compound of any one of claims 13-34, wherein the compound comprises one or more isotopically labeled atoms.

36. The compound of claim 35, wherein the isotopically labeled atom is 1 N, C, F, or 2H .

37. A method for identifying a target protein of a small molecule, the method comprising: (i) providing a compound comprising the small molecule connected to a photo-click tag via a linker, wherein the photo-click tag comprises (a) a diazirine moiety, and (b) a click chemistry handle; (ii) activating the diazirine moiety by irradiating the compound of (i) with a specific wavelength of light, (iii) contacting the target protein with the activated compound of (ii); (iv) forming a complex through a photo-induced covalent bond between the activated compound of (ii) and the protein; and (v) identifying the complex produced in (iv) that is bound to the compound, thereby identifying the target protein of the small molecule.

38. A method for identifying the binding site of a small molecule on a protein, the method comprising: (i) providing a compound comprising the small molecule connected to a photo- click tag via a linker, wherein the photo-click tag comprises (a) a diazirine moiety, and (b) a click chemistry handle; (ii) activating the diazirine moiety by irradiating the compound of (i) with a specific wavelength of light, (iii) contacting the protein with the activated compound of (ii); (iv) forming a complex through a photo-induced covalent bond between the activated compound of (ii) and the protein; (v) digesting the protein of the complex into constitutive peptides in the presence of a protease; and (vi) identifying the one or more peptides produced in (iv) that is bound to the compound, thereby identifying the protein binding site of the small molecule.

39. The method of claim 37 or 38, wherein the diazirine moiety forms a reactive carbene species upon irradiation with the specific wavelength of light

40. The method of any o e of claims 37-39, wherein the reactive carbene species reacts with a C-C, C-H, N-H, or Q-H bond of the protein.

4 1. The method of claim 40, wherein a new covalent bond is formed between the photo- click tag and the protein.

42. The method of any one of claims 37-41, wherein the specific wavelength of light is between about 0 nm and about 400 nm. 43. The method of claim 42, wherein the specific wavelength of light is between about 355 nm and about 365 nm.

44 The method of claim 37 or 38, wherein the click chemistry handle is an alkyne.

method of claim 37 or 38, wherein the photo-click tag of (i) is of the formula:

specific wavelength of light.

N

The method of any one of claims 37-45, wherein the diazirine moiety forms the reactive carbene species upon irradiation with the specific wavelength of light.

47. The method of claim 38, wherein the protease is a serine protease, cysteine protease, threonine protease, aspartic protease, glutamic protease, metal!oprotease, or an asparagine peptide lyase.

48. The method of claim 47, wherein the serine protease s trypsin.

49. The method of claim 37, wherein the identifying of step (v) comprises performing mass spectrometry to identify the proteins produced in (v) that are bound to the compound.

50. The method of claim 49, wherein the mass spectrometiv is intact mass spectrometry.

51. The method of claim 38, wherein the digesting of step (v) is performed under conditions suitable for the protease to catalyze the cleavage of peptide bonds in the protein. 52. The method of claim 38, wherein the identifying of step (vi) comprises separating the peptides produced in (v) that are bound to the compound from peptides that are not bound to the compound.

53. The method of claim 38 or 52, wherein the identifying of step (vi) comprises performing mass spectrometry to identify the peptides produced in (v) that are bound to the compound.

54. The method of claim 53, wherein the mass spectrometry is mass-independent mass spectrometry.

59. The method of claim 37 further comprising a step of enriching the complex formed in step (v).

60. The method of claim 38 further comprising a step of enriching the complex formed in step (iv).

61. The method of claim 60, wherein the enriching is performed before the digesting of step (v).

62. The method of claim 60, wherein the enriching is performed after the digesting of step

(v).

63. The method of any one of claims 59-62, wherein the enriching comprises covalently attaching a label to the click chemistry handle of the photo-click tag.

64. The method of claim 63, wherein the label comprises an affinity tag.

65. The method of claim 64, wherein the affinity tag is biotin.

66. The method of any one of claims 63-65, wherein the label comprises an azide moiety.

67. The method of any one of claims 63-66, wherein the label is of the formula: 68. The method of any one of claims 63-67, wherein the label s attached to the click chemistry handle of the photo-click tag using copper(i)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction conditions.

69. The method of claim 63-68 further comprising separating the complex using affinity chromatography.

70. The method of claim 69, wherein the affinity chromatography uses a column comprising streptavidin-coupled beads

7 1. The method of claim 37 or 38, wherein the protein is present in a whole proteome.

72. The method of claim 37 or 38, wherein the protein is present in a cell.

73. The method of claim 37 or 38, wherein the protein is present in a cell lysate.

74. The method of claim 72 or 73, wherein the cell is a mammalian ceil.

75. The method of claim 74, wherein the mammalian cell is a human ceil.

76. The method of claim 37 or 38, wherein the protein is in vitro.

77. The method of claim 37 or 38, wherein the protein is in vivo.

78. A method for identifying an interaction between a first protein and a second protein in a cell, the method comprising: (i) providing the cell with an amino acid analog, wherein the amino acid analog comprises a photo-click tag comprising (a) a diazirine moiety, and (b) a click chemistry handle, and wherein the amino acid analog is incorporated into the first protein and/or the second protein during protein synthesis, (ii) activating the diazirine moiety of the amino acid analog by irradiating the cell with a specific wavelength of light, (iii) contacting the first protein or the second protein with the activated compound of (ii);

(iv) forming a protein-protein complex through a photo-induced covalent bond between the activated amino acid analog of the first protein and an amino acid in the second protein; and (v) identifying the complex produced in (ii) that comprises the amino acid analog covalently linking the first protein and the second protein, thereby identifying the first protein and the second protein involved in the interaction.

79. The method of claim 78 further comprising digesting the protein-protein complex of (iii) into constitutive peptides in the presence of a protease; and (iv) identifying a conjugated peptide that comprises a peptide comprising the amino acid analog covalently linking a peptide of the first protein to a peptide of the second protein.

80. The method of claim 78, wherein the diazirine moiety forms a reactive carbene species upon irradiation with the specific wavelength of ligh

81. The method of claim 80, wherein the reactive carbene species reacts with a C-C, C-

H, Ν--Ή , or O-H bond of the first protein or the second protein.

82. The method of claim 81, wherein the amino acid analog is incorporated into the first protein during protein synthesis, and wherein a new covalent bond is formed between the photo-click tag of the amino acid analog and the second protein.

83. The method of claim 81, wherein the amino acid analog is incorporated into the second protein during protein synthesis, and wherein a new covalent bond is formed between the photo-click tag of the amino acid analog and the first protein,.

84. The method of any one of claims 78-83, wherein the specific wavelength of light is between about 10 nm and about 400 nm. 85. The method of claim 84, wherein the specific wavelength of light is between about 355 nm and about 365 nm.

86. The method of claim 78, wherein the click chemistry handle is an alkyne.

87. The method of claim 78, wherein the amino acid analog of (i) comprises the structure of

Formula (Π -a):

wherein P is the photo-click tag.

88 The method of claim 87, wherein P is of the formula:

before irradiation with the specific wavelength of light.

89. The method of any one of claims 78-88, wherein the amino acid analog of (i) is of the formula:

before irradiation with the specific wavelength of light.

N-N

90. The method of any one of claims 78-89, wherein the diazirine moiety ¾ forms the reactive carbene species with the specific wavelength of light. 9 1. The method of claim 78, wherein the protease is a serine protease, cysteine protease, threonine protease, aspartic protease, glutamic protease, metall oprotease, or an asparagine peptide lyase.

92. The method of claim 91, wherein the serine protease is trypsin.

93. The method of claim 78, wherein the digesting step is performed under conditions suitable for the protease to catalyze the cleavage of peptide bonds in the protein-protein complex.

94. The method of claim 78, wherein the identifying step comprises performing mass spectrometry to identify the conjugated peptide that comprises a peptide comprising the amino acid analog covalentiy linked to a peptide of the second protein.

95. The method of claim 94, wherein the mass spectrometry is mass-independent mass spectrometry.

96. The method of claim 78 further comprising a step of enriching the complex formed in step (iii).

97. The method of claim 96, wherein the enriching comprises covalentiy attaching a label to the click chemistry handle of the photo-click tag.

98. The method of claim 97, wherein the label comprises an affinity tag.

99. The method of claim 98, wherein the affinity tag is biotin.

100. The method of any one of claims 97-99, wherein the label comprises an azide moiety.

101 . The method of any one of claims 97-100, wherein the label is of the formula: : 102. The method of any one of claims 97-101, wherein the label is attached to the click chemistry handle of the photo-click tag using copper(i)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction conditions.

103. The method of claim 97-102 further comprising separating the complex using affinity chromatography.

104. The method of claim 103, wherein the affinity chromatography uses a column comprising streptavidin-coupled beads

105. The method of any one of claims 78-104 further comprising contacting the cell with a small molecule, wherein the cell is contacted with the small molecule before the activating of step (ii).

106. The method of claim 105, wherein the first protein and the second protein identified in the presence of the small molecule are compared to the first protein and the second protein identified in the absence of the small molecule.

07. The method of claim 106, wherein a difference in the first protein and the second protein in the presence of the small molecule compared to the first protein and the second protein in the absence of the small molecule indicates modulation of a protein-protein interaction in the cell in the presence of a small molecule.

108. The method of any one of claims 105-107, wherein the small molecule is an anti inflammatory agent, an immunomodulatory drug, a chemotherapeutic agent, or a derivative thereof. 109. The method of claim 78, wherein the first protein and the second protein are present in a whole proteome.

110. The method of claim 78, wherein the first protein and the second protein are present in a cell.

111. The method of claim 78, wherein the first protein and the second protein are present in a cell lysate.

2 . The method of claim 0 or 1 , wherein the ceil is a mammalian cell.

113. The method of claim 12, wherein the mammalian cell is a human cell.

4 . The method of claim 78, wherein the first protein and the second protein are present

/ / vivo.

5. A kit comprising the photo-click tag of any one of claims 1-12.

6 . A kit comprising the compound of any one of claims 13-36.

7. A kit for use in performing the method of any one of claims 37-77.

8. A kit for use in performing the method of any one of claims 78-1 14.