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A synopsis of the different screening stages is represented in figure 52.

Figure 52 - Schematic representation of the followed screening stages.

Hence, we decided to conduct qPCR measurements of mRNA transcripts (fig. 53) and/or to evaluate expression at the protein level by WB (fig. 54, 55, 56, 57 and 58) according to antibody availability, for correlation of observed phenotype with gene knockdown level for the twelve mentioned . The obtained results are summarized in table 12.

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Figure 53 - mRNA expression as determined by qPCR following infection of BMDCs with lentiviruses expressing shRNAs targeting the indicated genes. Constructs producing best phenotype are boxed. ND - not detectable. * - shRNA targeting 3’ UTR. Data are from one of at least 2 independent experiments.

Figure 54 - Protein expression measured by Western Blot for Degs1.

Figure 55 - Protein expression measured by Western Blot for β2m.

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Figure 56 - Protein expression measured by Western Blot for Rab2.

Figure 57 - Protein expression measured by Western Blot for Bet1.

Figure 58 - Protein expression measured by Western Blot for Vamp4.

Table 12 – Summary for gene knockdown level correlation with phenotype for hit genes (in brackets is indicated shRNA number that provided observed phenotype).

Gene symbol Knockdown correlation

Bet1 (3, 4, 5) Correlates

Degs1 (2, 3, 5) No Correlation

Dnm1 (2, 4) No Correlation

Rab17 (2, 5) No Correlation

Rab19 (1-5) Correlates

Rab2 (3, 4) Possible Correlation

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Rab40b (1, 2, 4) Possible Correlation

Sec24d (1, 3, 4, 5) No Correlation

Stx18 (3, 5) Possible Correlation

Vamp4 (1-5) Correlates

Vti1a (3, 4) Correlates

β2m (2, 5) Possible Correlation

Taken together, four genes showed a good correlation between knockdown level and phenotype: Vamp4, Rab19, Vti1a and Bet1; four others (Rab40b, Rab2, β2m, Stx18) showed potential correlations, i.e., some of the constructs that produced a phenotype did not produced the lowest mRNA levels, which may be explained by differential lentiviral knockdown efficiencies along different experiments, or additional effects at the translational level. Further validation using immunobloting will be required to clarify if these genes are true hits. Interestingly, constructs targeting the 3’ UTR (indicated with “*” in fig. 53) are in many cases those that either produce one of the best knockdowns or the gene mRNA level is the same (or higher) when compared to control. The observation that some shRNAs used for gene targeting produce higher mRNA levels when compared to the control has been previously described when using this strategy (Oberdoerffer et al., 2008). One possible explanation might be due to a miRNA effect, as there have been reports describing these as transcriptional up-regulators (Vasudevan et al., 2007), although this is speculative in this context. Also, in the case of Vamp4, the Western blot showed that reduced transcript expression was accomplished by all shRNA hairpins, Vamp4 was just depleted at the protein level by construct #II, #III and #V.

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At this point, we decided to focus in the gene Vamp4 (vesicle-associated membrane protein 4), which has been suggested to play a role in the trans-Golgi network-to-endosome transport (Tran et al., 2007). The rationale for this decision is based in: 1) the strength of the phenotype and knockdown correlation; 2) when analyzing known and predicted protein-protein interactions databases (Jensen et al., 2009), we could observe that we “hited” another interacting gene, Vti1a, along with the fact that Snap25, Stx1b2, Stx3, Stx6, Stx1b1 and Stx4 also matched the selection criteria for the secondary screening, even though the first four possibly also affect class II presentation as well, and the last two provided inconclusive results. The Vamp4 interacting network is depicted in figure 59.

Figure 59 - Known and predicted interactions for Vamp4 protein. From http://string.embl.de (Jensen et al., 2009).

As antibodies targeting Snap23 (another of the described interactors of Vamp4, fig. 59) and Stx6 were available, we also decided to investigate their knockdown level by western blot (fig. 60 and fig. 61) using our shRNA lentiviral system, in order to pursue further antigen presentation experiments in the Vamp4 interacting complex.

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Figure 60 - Protein expression measured by Western Blot for Snap23.

Figure 61 - Protein expression measured by Western Blot for Stx6.

As we can observe from figs. 60 and 61, constructs #1 and #5 targeting Snap23 produce lower protein levels when compared to control, while none of the Stx6 shRNA targeting hairpins mediate protein knockdown. The validated candidates are now good candidates for follow-up mechanistic studies (using biochemistry and cell biology tools) and to be tested in an in vivo relevant model of antigen cross-presentation.

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Concluding remarks and future perspectives

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168 III. Concluding remarks and future perspectives

Chapter III – Concluding remarks and future perspectives

The work reported here (both for the /phosphatase subset and for the cellular traffic collection of genes) is, to our knowledge, the first systematic screen that aims to identify genes with a role in antigen presentation in primary cells. Particular effort has been made in the recent past to identify genes involved in antigen cross-presentation, in a more restrictive and direct manner (Guermonprez et al., 2003; Jancic et al., 2007; Luckashenak et al., 2008). Recently, (Zou et al., 2009) reported the identification of a new gene (Rab3b/3c) with a role in cross-presentation in dendritic cells, targeting a much smaller collection of genes (57) than the ones reported in this work and by using a murine dendritic cell-line (DC2.4) as APC.

Our results suggest that no kinase or phosphatase affects, in a specific manner, cross-presentation, even if I have identified many with a phenotype for both canonical and antigen cross-presentation pathways. Indeed, when considering the role of (major signal transducers) within the endocytic machinery (which is in fact the underlying basis of antigen presentation), one could predict many interaction points between both and specificities. Interestingly enough, when (Liberali et al., 2008) collected all known direct phosphorylation reactions of endocytic machinery components assigned to specific protein kinases from the literature, and annotated those kinases onto the protein kinome tree, they observed that there is not one specific class of kinases that phosphorylates endocytic machinery. Rather, kinases are distributed along the tree, suggesting that the diversity of both has coevolved. In addition, it has to be taken into account that many studies are actually conducted in cancer cells and that the kinases involved in a particular process in transformed cells may be quite different from the ones regulating the same process in primary cells.

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Currently, there is little to no information on the genes that regulate membrane transport and are critically involved in cross-presentation. Therefore, the identification of 8 novel genes with a specific or predominantly specific role in antigen cross-presentation is of particular relevance. It is particularly exciting the identification of Vamp4, especially because seven of its predicted molecular interactions also give a phenotype when silenced in our screen.

Overall, our work has identified ~80 novel genes with a role in antigen presentation and ~8 with a specific role predominantly in antigen cross- presentation. This achievement represents a potential enormous advance to this field as it raises an unprecedented number of molecular leads that have the potential to help the community working in this field to begin to understand the pathways that are specifically involved and required for antigens to be cross- presented.

This is however the very beginning! My findings are the starting point for many possible ways in which this project can evolve. No doubt, the first important follow-up study will be to use biochemistry and cell biology tools to understand the fine molecular mechanisms and pathways that are regulated by the identified genes in the context of antigen cross-presentation.

The second major axis of research to which my work can give rise is the study of the role of the now identified genes in vivo. Several biologically significant problems or models can be selected, but they should reflect relevant questions in the field including the response to tumors, non-infecting APC virus and against parasites. A good example could be the role of these genes in an in vivo response against Toxoplasma gondii. Interestingly, it has recently been shown that the recruitment of ER is abundant and critical to generate CD8+ T cell responses against this parasite in vitro and in vivo (Goldszmid et al., 2009). There has been a long-standing controversy on the literature about the role of the ER in antigen cross-presentation. Our screen identifies several genes

170 III. Concluding remarks and future perspectives

(belonging to the vesicular traffic set) that are known to be involved in ER to other vesicle fusion and that localize to the ER. We are currently exploring this possibility with our collaborators at the Curie Institute (Dr. Sebastian Amigorena’s Group).

Our own laboratory is currently working on a technology that will help us to dissect the role of the identified genes in antigen cross-presentation in vivo: using a lentiviral system that can be controlled spatially and temporally, we expect to be able to silence our gene of interest in the relevant cells for antigen presentation (Dendritic Cells) and switch it on and off with the addition or removal of a drug (tetracycline). With this tool in our hands, it will be possible to expand the work to genes for which classical homologous recombination knockouts are not available and also for those that are required for animal viability. This is also a powerful approach, because we can study the role of a gene in a specific cell type at a particular time.

Finally, but importantly, we will use drugs that are known to block genes or the pathways that we have identified and use them to probe their effect in in vitro assays for antigen presentation. Should any of this give a strong phenotype in vitro, we will probe their effect in the in vivo models of tumor response, currently under construction. Our preliminary results using a restricted number of kinase inhibitors that have reproduced the phenotypes observed by the shRNA silencing, strongly suggest that this will be a powerful line of work.

I am confident that this integrated strategy for the follow-up of the work here presented has the potential to greatly improve our knowledge about antigen cross-presentation and its relevance in the generation of effective CTL responses against tumors and viral infections.

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Chapter IV

Materials and Methods

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IV. Materials and Methods

174 IV. Materials and Methods

Chapter IV – Materials and Methods

Mice C57BL/6 mice (WT) were obtained from Instituto Gulbenkian de Ciência. C57BL/6 recombination activating gene 1-deficient OT-1 TCR and C57BL/6 recombination activating gene 2-deficient OT-2 TCR transgenic mice were obtained from Taconic and The Jackson Laboratory. All mice were used according to the guidelines and regulations of the Portuguese Veterinary Department.

Purification of bone marrow derived dendritic cells Purification of bone marrow derived cells (BMDCs) was adapted from previously described (Inaba et al., 1992; Inaba et al., 2001). Briefly, marrow cavities of the tibias and femurs of 8-12 week-old mice were flushed with complete RPMI 1640 (10% FBS) using a 27-gauge needle (Terumo, Tokyo, Japan). After red cells hypotonic lysis for 5 min (with ammonium chloride solution), BM cells were washed and seeded in 96 well round bottom plates (5x104/well), in culture medium supplemented with 30% conditioned medium from mouse granulocyte-macrophage colony stimulating factor (GM-CSF) producing J558L cells.

T-cells purification Spleens were isolated from OT-I or OT-II mice. Individual cell suspensions were obtained by disrupting the spleens in RPMI and forcing them through a 70 µm cell strainer. The cells were spun at 1,200 RPM for 5 minutes and the resulting cell suspensions were subjected to hypotonic red cell lysis. The cells were washed and resuspended in PBS (supplemented with 5% FBS), and negatively isolated using magnetic beads, (CD8 and CD4 isolation kits, Miltenyi Biotec, Auburn, CA, purification >90%), according to manufacture’s protocol.

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Viral production Plasmids encoding lentiviruses expressing shRNAs were obtained from the RNAi Consortium library (TRC), supplied as glycerol stocks (Moffat et al., 2006). Plasmids were purified using a 96 well plate format DNA extraction procedure according to the public protocol described by the TRC

(http://www.broad.mit.edu/genome_bio/trc/publicProtocols.html) and DNA was quantified by a Pico-Green assay (Molecular Probes), using a Infinite M200 plate reader (Tecan). DNA concentrations were normalized manually across plates. Plasmids were then transfected into HEK 293T cells with a three-plasmid system to produce lentivirus (Dull et al., 1998; Naldini et al., 1996). Transfections were performed in 96-well plates to generate lentiviruses in a high-throughput manner as adapted by (Moffat et al., 2006). Briefly, packaging cells were seeded at a density of 2.2x104 cells per well in 100µl media (DMEM, 10% FBS, no

antibiotics) 24 hours before transfection and grown at 37ºC, 5% CO2. DNA for transfections was prepared by mixing 100ng pCMVΔR.89 and 10ng pVSV-G with 100ng pLKO.1 library plasmids in each well. A mixture of 24.26µl OptiMEM (Gibco) and 0.6µl TransIT-LT1 (Mirus) were then added to the DNA and this mixture was incubated for 30 min before addition to the packaging cells. Cells were incubated for 24 h, and the media was changed to remove remaining transfection reagent, with addition of fresh media, supplemented with 30% FBS. Cell supernatants containing the viral particles were collect 48 and 72h after transfection and stored at -80ºC.

shRNA lentiviral infections Mouse BMDCs were plated in 96 well round-bottom plates at 5x104 cells per well with 200µl of GM-CSF supplemented medium. After 48h, the medium was carefully removed without disturbing the cells at the bottom, and the cells were infected using 10µl of shRNA lentiviral supernatant (the pellet was ressuspended 3-5 times) plus 8µg/ml of polybrene (hexadimethrine bromide) (Sigma) in 40µl of GM-CSF medium. The cells were spun for 90 min at 2200 rpm, after which cell

176 IV. Materials and Methods supernatant was removed and 200µl/well of fresh media was added. To select for shRNA integration, 48h after infection, puromycin (Calbiochem) was added at a final concentration of 5 µg/ml. The cells were challenged 4 days after infection.

Antigen presentation assays Materials: OVA (Worthington Biochemical Corporation); S. cerevisiae expressing OVA (kindly provided by Dr. R. Wheeler, WI); OVA peptide 257- 264 (SIINFEKL) (Neaps); OVA peptide 323-339 (Neaps). For antigen presentation assays, BMDCs were incubated with the indicated antigen sources and concentrations. Approximately 4h later, cells were co- cultured with labeled CFSE (carboxyfluorescein diacetate, succinimidyl ester, which upon processing, is a green fluorescent cell staining dye) (Invitrogen) OT- I T cells for 3 days. CFSE passively diffuses into cells and is retained throughout development and meiosis. The dye is inherited by the daughter cells, and after each cell division, the relative fluorescence intensity of the dye is decreased by half, which can be visualized in a FACS plot as different fluorescence peaks. For monitoring T cell proliferation, diminution of CFSE staining on TCR+ CD8+ population was measured by FACS. In alternative, cell cultures were pulsed with 1 µCi [3H] thymidine (Perkin Elmer) for approximately 12 hr, and incorporation of the radionucleotide was measured using a β-scintillation counter (TopCount Gamma Counter; Packard, MA, USA). In addition, cell supernatants were collected for IL-2 and IFN-γ cytokine measurement. Similar procedure was followed in monitoring OT-II T cell proliferation.

Moreover, antigen presentation assays were also conducted by incubating BMDCs for 18h with the B3Z cell line, CD8+ T-cell hybridoma specific for H- 2Kb OVA 257-264 complex. B3Z activation was monitored by IL-2 secretion as measured by ELISA.

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Antigen processing assays

Materials: DQ™ ovalbumin (Invitrogen). For antigen processing assays, BMDCs were incubated with DQ™ ovalbumin (0.25µg/ml) for 4h, after which fluorescence emission was measured. DQ™ ovalbumin is a self-quenched conjugate of ovalbumin that exhibits bright green fluorescence upon proteolytic degradation (fluorescence excitation and emission maxima of approximately 505 and 515 nm, respectively).

Cell viability assay Cell number is assessed through Alamar Blue™ (Biosource, Camarillo, CA) staining. Alamar Blue™ contains a redox indicator that fluoresces during respiration of assay cells. It can accurately measure cell numbers as low as a few hundred. Fluorescence is excited at 530-560 nm and emitted at 590 nm. A series of standard known number of cells are prepared in addition to the samples and jointly incubated with the Alamar Blue™ dye for 2h (1:20), followed by fluorescence reading.

Yeast growth S. cerevisiae expressing OVA strain was maintained in Synthetic Complete (SC) medium (Q-BIO Gene, USA), supplemented with glucose (for OVA expression inhibition) and a “drop-out” mix with exception of URA. S. cerevisiae was grown overnight in SC medium, supplemented with galactose (for OVA expression) at 30°C. Overnight cultures were diluted 1:50 into fresh SC+galactose-URA media and grown overnight.

Inactivation of yeast for antigen presentation experiments For UV inactivation, the equivalent of 2.5×107 cells from a culture were washed and resuspended in 1.5 ml of PBS in a six-well plate. The yeast were exposed to four treatments of 100,000 µjoules/cm2 in a CL-1000 UV-Crosslinker (UVP,

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Upland, California, United States), with agitation between each dose to treat cells evenly. After UV-inactivation, cells were washed and renormalized by OD600.

Quantitative RT-PCR Total RNA was extracted using Trizol according to the manufacturer ’ s protocol (Invitrogen), and each sample (1 µg) was reverse transcribed with SuperScript II (Invitrogen) using Oligo-DTTs (Invitrogen) according to the manufacturer’s instructions. Oligonucleotide primers were determined using Primer Bank, available at http://pga.mgh.harvard.edu/primerbank/ (Spandidos et al., 2008; Wang and Seed, 2003) and obtained from Invitrogen. The 25µl QPCR reaction (contained 1 µl of cDNA, 12.5 µl of SYBR green master mix (Applied Biosystems), and 20 pmol of sense and antisense primers) was performed on an Abi Prism 7000 (Applied Biosystems, Foster City, CA). An initial activation step for 10 min at 95°C was followed by 40 cycles of (95°C, 15 sec; 60°C, 60 sec). Quantity values for gene expression were generated by comparison of the fluorescence generated by each sample (always run in triplicate) with standard curves of known quantities (the standard series were prepared by performing 10-fold serial dilutions of full-length cDNAs per QPCR reaction), and the calculated number of copies was divided by the number of copies of the housekeeping gene GAPDH. Primers sequences:

Gene Sequences Acvr2a Fw: GCGTTCGCCGTCTTTCTTATC Rv: GTTGGTTCTGTCTCTTTCCCAAT Bet1 Fw: GGGCTTTGAATTTGTTGCAT Rv: GGGAAACCCTGGAAAAACAT Dmpk Fw: CTGCTCGACCTTCTCCTGG Rv: CACGCCCGATCACCTTCAA Dnaja2 Fw: GTTAGCCAAAGAATACCACCCTG Rv: TCTGTCATACAGCTCTCGCTT Dnajb8 Fw: ACAAGAACCCCGACAACAAAG Rv: CGGTCGTACACAGAACGCTT Dnajc7 Fw: AGTGCGATGTGGTAATGGCG Rv: GCTTCGTTGTAGTCCTTCTTAGC Dnm1 Fw: AATATGCCGAGTTCCTGCACT Rv: GTCTCAGCCTCGATCTCCAG Doc2b Fw: CGACGGCTACGAGTCAGAC Rv: TTCAGGGTGTTCCGAAGAGTT Erbb3 Fw: AAGTGACAGGCTATGTACTGGT Rv: GCTGGAGTTGGTATTGTAGTTCA GAPDH Fw: AACTTTGGCATTGTGGAAGG Rv: ACACATTGGGGGTAGGAACA

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Gcs1 Fw: CACGTCTATTTCGGCATGAAGA Rv: TGCCTGAGCTTAGGAGGGG Gucy1b2 Fw: TGATGTCTGAAGTGTTGTGTGC Rv: GCTTGCTCCTAAACTCCGCTC Mapk7 Fw: GTGGGGGACGAGTACGAGAT Rv: TGGTCACCACATCAAAAGCAT Pdpk1 Fw: GGTCCAGTGGATAAGCGAAA Rv: TTTCTGCACCACTTGTGAGC Pim2 Fw: TTCAGCGGGCTCAATATACGC Rv: CCAAGTCGGTATTCGGCCTC Rab17 Fw: GGCCCTCCGGTACATGAAG Rv: GGCACCCCTGAAGTAGAGGT Rab19 Fw: GTTCAAGGTCATCCTTATTGGGG Rv: GCACTCCGGTAGTAGCTTTGG Rab2 Fw: GCGACACAGGTGTTGGTAAAT Rv: CATCAATCGTTATCATCCGAGCA Rab40b Fw: GTGCGGGCCTACGATTTTCTA Rv: GTGGCCGTAAGGAGACTCG Sec24d Fw: GGAGAGGTCTTTGTTCCTTTGTT Rv: GTCTCTGTTCTTGAGCTTCCC Stx18 Fw: CCCACAAGGAGATACATTCCCA Rv: AACGAAATCCAAAACGGCAGT Vamp4 Fw: CGAAGGCAAATGTGGTGGC Rv: TTTCAAGTGCAGGATGATCTGAG Vdac3 Fw: TTGACACAGCCAAATCCAAA Rv: GCTGTCCATGCCAGGTTTAT Vti1a Fw: GGATCGCCTACAGTGACGAAG Rv: CAGCCTCTCCGTGTTATCCAG β2m Fw: TTCTGGTGCTTGTCTCACTGA Rv: CAGTATGTTCGGCTTCCCATTC

Western Blots Antibodies: Rabbit polyclonal anti-PDK1 (Abcam), mouse monoclonal anti- Pim2 (Abcam), rabbit polyclonal anti-Vamp4 (Abcam), rabbit monoclonal anti- β2m (Abcam), mouse monoclonal anti-Degs1 (Abcam), goat polyclonal anti- Rab2 (Abcam), mouse monoclonal anti-Bet1 (BD Biosciences), mouse monoclonal anti-Stx6 (Abcam), rabbit polyclonal anti-Snap23 (Abcam), mouse monoclonal anti-β-actin (Abcam), rabbit anti-α/β tubulin (Cell Signaling); anti- mouse, anti-rabbit and anti-goat secondary antibodies (Cell Signaling). All antibodies were used according to manufactures recommendations. Cells were harvested by centrifugation (1200 rpm, 5 minutes, room temperature), after which were rinsed once with phosphate buffered saline (PBS). Cell pellets were then lysed in 20-40µL of lysis buffer (50mM Tris, pH 7.4, 150 mM NaCl, 1% NP40, 0.25% sodium deoxycholate, 1mM EGTA, 1mM

PMSF, protease inhibitors, 1mM Na3VO4, 1mM NaF), incubated 10min on ice and centrifuged at 14000 rpm (10 min, 4ºC). The resulting supernatants were transferred to a fresh 1.5mL tube. Samples were loaded on 10-12% SDS-PAGE gel and after transferring, the membranes were blocked and incubated with primary antibodies. Anti-actin immunoblotting served as a loading control for the Western blots, unless if otherwise stated. Immunoblots were developed using horseradish peroxidase–coupled secondary

180 IV. Materials and Methods antibodies and detected by enhanced chemiluminescence (GE Healthcare, Piscataway, NJ).

Cytokine production measurement Cell supernatants were collected at the referred antigen presentation assay time points and analyzed for TNF-α, IL-6, IL-12, IL-2 and IFN-γ using DuoSet ELISA reagents according to the manufacture’s protocol (R&D systems, Minneapolis, MN).

Flow cytometry Cells were stained with indicated antibodies for 20 min, on ice. After washing, the cells were ressuspended in PBS (FBS 5%) and subsequently measured using a FACSCalibur flow cytometer (BD Biosciences, San Jose, CA) and analyzed using the FlowJo software (TreeStar, Ashland, OR). APC-conjugated anti-CD11c (Biolegend), PE-conjugated anti-CD11c (eBiosciences), FITC-conjugated anti-CD86 (eBioscience), FITC-conjugated anti- I-A^b (BD Biosciences), FITC-conjugated anti-H-2K^b (BD Biosciences) and FITC-conjugated anti-Vβ8 TCR (BD Biosciences) were used at 1 mg/ml.

Statistical analysis

The data were analyzed using the Prism software and compared using the Mann-Whitney U test, a nonparametric test that does not assume Gaussian variation.

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Supplementary Data

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184 V. Supplementary Data

Chapter V – Supplementary Data

Figure S1 – Plate-well scatter plot raw data of BMDCs number for replicate 1.

Figure S2 – Plate-well scatter plot raw data of BMDCs number for replicate 2.

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Figure S3 – Plate-well scatter plot raw data of T-cell proliferation for replicate 1.

Figure S4 – Plate-well scatter plot raw data of T-cell proliferation for replicate 2.

186 V. Supplementary Data

Table S1 – Gene list of enriched kinase/phosphatase screened subset.

Gene Gene Description NM number 4.93E+23 hypothetical protein 4933423E17 NM_177706 1110020G09Rik RIKEN cDNA 1110020G09 gene XM_127934 1190002A17Rik RIKEN cDNA 1190002A17 gene XM_130050 1700011K15Rik RIKEN cDNA 1700011K15 gene NM_029294 1810024B03Rik RIKEN cDNA 1810024B03 gene NM_198630 1810043M15Rik RIKEN cDNA 1810043M15 gene NM_199056 2310009E04Rik RIKEN cDNA 2310009E04 gene XM_131496 2610018G03Rik RIKEN cDNA 2610018G03 gene NM_133729 2610019A05Rik RIKEN cDNA 2610019A05 gene NM_028126 2610311B01Rik RIKEN cDNA 2610311B01 gene XM_355379 2700092H06Rik RIKEN cDNA 2700092H06 gene XM_132529 2810465F10Rik RIKEN cDNA 2810465F10 gene XM_127419 3110003A22Rik RIKEN cDNA 3110003A22 gene NM_026534 4732472I07Rik RIKEN cDNA 4732472I07 gene XM_195168 4921509C19Rik RIKEN cDNA 4921509C19 gene NM_198655 4921528H16Rik RIKEN cDNA 4921528H16 gene XM_133060 4930444A02Rik RIKEN cDNA 4930444A02 gene NM_029037 4930509O22 hypothetical protein 4930509O22 NM_172504 4930513D10Rik RIKEN cDNA 4930513D10 gene XM_142762 4932414J04 hypothetical protein 4932414J04 NM_172792 4932415M13 hypothetical protein 4932415M13 NM_177599 4933425A18Rik RIKEN cDNA 4933425A18 gene XM_127578 4933428I03Rik RIKEN cDNA 4933428I03 gene NM_025760 6330514A18Rik RIKEN cDNA 6330514A18 gene NM_183152 6720485C15Rik RIKEN cDNA 6720485C15 gene NM_026551 A630047E20Rik RIKEN cDNA A630047E20 gene NM_173032 Aatk apoptosis-associated NM_007377 v-abl Abelson murine leukemia oncogene Abl1 NM_009594 1 v-abl Abelson murine leukemia viral Abl2 XM_136360 oncogene 2 (arg, Abelson-related gene) Acacb acetyl-Coenzyme A carboxylase beta NM_133904 Acp1 acid phosphatase 1, soluble NM_021330 Acvr1 activin A receptor, type 1 NM_007394 Acvr1b activin A receptor, type 1B NM_007395 Acvr1c activin A receptor, type IC XM_194020 Acvr2a activin receptor IIA NM_007396 Acvr2b activin receptor IIB NM_007397 Acvrl1 activin A receptor, type II-like 1 NM_009612 a disintegrin and metallopeptidase domain Adam22 XM_131876 22 Adck1 aarF domain containing kinase 1 NM_028105 Adck2 aarF domain containing kinase 2 NM_178873 Adck4 aarF domain containing kinase 4 NM_133770 Adck5 aarF domain containing kinase 5 NM_172960 Adk NM_134079 Adpgk ADP-dependent NM_028121 Adrbk1 adrenergic receptor kinase, beta 1 NM_130863 Adrbk2 adrenergic receptor kinase, beta 2 NM_177078 AIF1 allograft inflammatory factor 1 NM_001623

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Ak1 1 NM_021515 Ak2 adenylate kinase 2 NM_016895 Ak3 adenylate kinase 3 NM_021299 Ak3l1 adenylate kinase 3 alpha-like 1 NM_009647 Ak5 adenylate kinase 5 NM_153066 Akap2 A kinase (PRKA) anchor protein 2 NM_009649 Akt1 thymoma viral proto-oncogene 1 NM_009652 Akt2 thymoma viral proto-oncogene 2 NM_007434 Akt3 thymoma viral proto-oncogene 3 NM_011785 Alk anaplastic lymphoma kinase NM_007439 Alpk1 alpha-kinase 1 XM_131194 Alpk2 alpha-kinase 2 XM_128981 Alpk3 alpha-kinase 3 NM_054085 amyotrophic lateral sclerosis 2 (juvenile) Als2cr2 NM_172656 region, candidate 2 (human) amyotrophic lateral sclerosis 2 (juvenile) Als2cr7 XM_194683 chromosome region, candidate 7 Amhr2 anti-Mullerian hormone type 2 receptor NM_144547 Anapc2 anaphase promoting complex subunit 2 NM_175300 ankyrin repeat and kinase domain Ankk1 NM_172922 containing 1 Apoe apolipoprotein E NM_009696 v-raf murine sarcoma 3611 viral oncogene Araf NM_009703 homolog Arhgap24 Rho GTPase activating protein 24 NM_146161 Arhgap29 Rho GTPase activating protein 29 NM_172525 Arhgap5 Rho GTPase activating protein 5 NM_009706 Atf6 activating transcription factor 6 XM_129579 ataxia telangiectasia mutated homolog Atm NM_007499 (human) ATPase, Ca++ transporting, cardiac Atp2a2 NM_009722 muscle, slow twitch 2 Atp2a3 ATPase, Ca++ transporting, ubiquitous NM_016745 Atr ataxia telangiectasia and rad3 related XM_147046 Aurka aurora kinase A XM_130737 Aurkb aurora kinase B XM_181344 Aurkc aurora kinase C NM_020572 AW548124 expressed sequence AW548124 XM_128778 AW742319 expressed sequence AW742319 NM_021345 Axin2 axin2 NM_015732 Axl AXL receptor tyrosine kinase NM_009465 B230120H23Rik RIKEN cDNA B230120H23 gene NM_023057 Bace1 beta-site APP cleaving 1 NM_011792 Bag1 Bcl2-associated athanogene 1 NM_009736 BC021891 cDNA sequence BC021891 NM_145608 BC021917 cDNA sequence BC021917 NM_145496 BC030499 cDNA sequence BC030499 XM_126274 BC032265 cDNA sequence BC032265 NM_181420 BC052883 cDNA sequence BC052883 NM_201370 Bcap31 B-cell receptor-associated protein 31 NM_012060 branched chain ketoacid dehydrogenase Bckdk NM_009739 kinase Bcr breakpoint cluster region homolog XM_125706 Blk B lymphoid kinase NM_007549

188 V. Supplementary Data

BLNK B-cell linker NM_013314 Bmi1 B lymphoma Mo-MLV insertion region 1 NM_007552 Bmp2k BMP2 inducible kinase NM_080708 bone morphogenetic protein receptor, type Bmpr1a NM_009758 1A bone morphogenetic protein receptor, type Bmpr1b NM_007560 1B bone morphogenic protein receptor, type II Bmpr2 NM_007561 (serine/threonine kinase) Bmx BMX non-receptor tyrosine kinase NM_009759 Braf Braf transforming gene XM_355754 Brd2 bromodomain containing 2 NM_010238 Brd7 bromodomain containing 7 NM_012047 Brsk1 BR serine/threonine kinase 1 XM_356021 Bruton agammaglobulinemia tyrosine Btk NM_013482 kinase Btrc beta-transducin repeat containing protein NM_009771 C330002I19Rik RIKEN cDNA C330002I19 gene XM_126866 C330011J12Rik RIKEN cDNA C330011J12 gene XM_136225 C330018K18Rik RIKEN cDNA C330018K18 gene NM_177352 C330049O21Rik RIKEN cDNA C330049O21 gene NM_177174 Calm2 calmodulin 2 NM_007589 Calm3 calmodulin 3 NM_007590 Calr Calreticulin NM_007591 calcium/calmodulin-dependent protein Camk1 NM_133926 kinase I calcium/calmodulin-dependent protein Camk1d NM_177343 kinase ID calcium/calmodulin-dependent protein Camk1g NM_144817 kinase I gamma calcium/calmodulin-dependent protein Camk2a NM_009792 kinase II alpha calcium/calmodulin-dependent protein Camk2b NM_007595 kinase II, beta calcium/calmodulin-dependent protein Camk2d NM_023813 kinase II, delta calcium/calmodulin-dependent protein Camk2g NM_178597 kinase II gamma calcium/calmodulin-dependent protein Camk4 NM_009793 kinase IV calcium/calmodulin-dependent protein Camkk1 NM_018883 kinase kinase 1, alpha calcium/calmodulin-dependent protein Camkk2 NM_145358 kinase kinase 2, beta Camkv CaM kinase-like vesicle-associated NM_145621 Canx calnexin NM_007597 Carkl carbohydrate kinase-like NM_029031 calcium/calmodulin-dependent serine Cask NM_009806 (MAGUK family) Casp12 caspase 12 NM_009808 Ccnd1 cyclin D1 NM_007631 Ccrk cell cycle related kinase NM_053180 CD209 CD209 antigen NM_021155 cytidine and dCMP deaminase domain Cdadc1 XM_127813 containing 1

189

V. Supplementary Data

cell division cycle 20 homolog (S. Cdc20 NM_023223 cerevisiae) cell division cycle 25 homolog A (S. Cdc25a NM_007658 cerevisiae) cell division cycle 25 homolog B (S. Cdc25b NM_023117 cerevisiae) cell division cycle 25 homolog C (S. Cdc25c NM_009860 cerevisiae) Cdc2a cell division cycle 2 homolog A (S. pombe) NM_007659 Cdc2l1 cell division cycle 2-like 1 NM_007661 cell division cycle 2-like 5 (cholinesterase- Cdc2l5 XM_127221 related cell division controller) Cdc2l6 cell division cycle 2-like 6 (CDK8-like) NM_198164 Cdc42bpa Cdc42 binding protein kinase alpha XM_283677 Cdc42bpb Cdc42 binding protein kinase beta NM_183016 CDC42 binding protein kinase gamma Cdc42bpg XM_140553 (DMPK-like) Cdc7 cell division cycle 7 (S. cerevisiae) NM_009863 Cdk10 cyclin-dependent kinase (CDC2-like) 10 NM_194444 Cdk2 cyclin-dependent kinase 2 NM_016756 Cdk3 cyclin-dependent kinase 3 NM_027165 Cdk4 cyclin-dependent kinase 4 NM_009870 Cdk5 cyclin-dependent kinase 5 NM_007668 cyclin-dependent kinase 5, regulatory Cdk5r1 NM_009871 subunit (p35) 1 cyclin-dependent kinase 5, regulatory Cdk5r2 NM_009872 subunit 2 (p39) Cdk6 cyclin-dependent kinase 6 NM_009873 cyclin-dependent kinase 7 (homolog of Cdk7 NM_009874 Xenopus MO15 cdk-activating kinase) Cdk8 cyclin-dependent kinase 8 NM_153599 cyclin-dependent kinase 9 (CDC2-related Cdk9 NM_130860 kinase) cyclin-dependent kinase-like 1 (CDC2- Cdkl1 NM_183294 related kinase) cyclin-dependent kinase-like 2 (CDC2- Cdkl2 NM_016912 related kinase) Cdkl3 cyclin-dependent kinase-like 3 NM_153785 Cdkl5 cyclin-dependent kinase-like 5 XM_356367 CCAAT/enhancer binding protein (C/EBP), Cebpa NM_007678 alpha CCAAT/enhancer binding protein (C/EBP), Cebpb NM_009883 beta Cerk NM_145475 CFL1 cofilin 1 (non-muscle) NM_005507 CFL2 cofilin 2 (muscle) NM_021914 Chek1 checkpoint kinase 1 homolog (S. pombe) NM_007691 Chek2 CHK2 checkpoint homolog (S. pombe) NM_016681 Chka alpha NM_013490 Chkb choline kinase beta NM_007692 Cit citron NM_007708 Cbp/p300-interacting transactivator, with Cited4 NM_019563 Glu/Asp-rich carboxy-terminal domain, 4 Ckb , brain NM_021273 Ckm creatine kinase, muscle NM_007710

190 V. Supplementary Data

creatine kinase, mitochondrial 1, Ckmt1 NM_009897 ubiquitous Ckmt2 creatine kinase, mitochondrial 2 NM_198415 Cks1b CDC28 protein kinase 1b NM_016904 Cks2 CDC28 protein kinase regulatory subunit 2 NM_025415 Clk1 CDC-like kinase 1 NM_009905 Clk2 CDC-like kinase 2 NM_007712 Clk3 CDC-like kinase 3 NM_007713 Clk4 CDC like kinase 4 NM_007714 Cmpk NM_025647 connector enhancer of kinase suppressor of Cnksr2 NM_177751 Ras 2 Coasy Coenzyme A synthase NM_027896 Cpne4 copine IV XM_135115 Crebbp CREB binding protein XM_148699 Crk7 CDC2-related kinase 7 NM_026952 Crybb2 crystallin, beta B2 NM_007773 Csf1r colony stimulating factor 1 receptor NM_007779 Csk c-src tyrosine kinase NM_007783 Csnk1a1 casein kinase 1, alpha 1 NM_146087 Csnk1d casein kinase 1, delta NM_027874 Csnk1e casein kinase 1, epsilon NM_013767 Csnk1e casein kinase 1, epsilon NM_013767 Csnk1g1 casein kinase 1, gamma 1 NM_173185 Csnk1g2 casein kinase 1, gamma 2 NM_134002 Csnk1g3 casein kinase 1, gamma 3 NM_152809 Csnk2a1 casein kinase II, alpha 1 polypeptide NM_007788 Csnk2a2 casein kinase II, alpha 2, polypeptide NM_009974 Csnk2b casein kinase II, beta subunit NM_009975 catenin (cadherin associated protein), beta Ctnnb1 NM_007614 1, 88kDa Cul1 cullin 1 NM_012042 Cul2 cullin 2 NM_029402 Cul3 cullin 3 NM_016716 Cul4a cullin 4A NM_146207 Cul4b cullin 4B NM_028288 Cul5 cullin 5 NM_027807 Cul7 cullin 7 XM_358324 D830007F02Rik RIKEN cDNA D830007F02 gene NM_175441 disabled homolog 2 (Drosophila) Dab2ip XM_130206 interacting protein Dapk1 death associated protein kinase 1 NM_029653 Dapk2 death-associated kinase 2 NM_010019 Dapk3 death-associated kinase 3 NM_007828 double cortin and calcium/calmodulin- Dcamkl1 NM_019978 dependent protein kinase-like 1 Dcamkl2 doublecortin and CaM kinase-like 2 NM_027539 Dcamkl3 doublecortin and CaM kinase-like 3 NM_172928 Dck NM_007832 discoidin domain receptor family, member Ddr1 NM_007584 1 discoidin domain receptor family, member Ddr2 NM_022563 2 Dgka , alpha NM_016811

191

V. Supplementary Data

Dgkb diacylglycerol kinase, beta NM_178681 Dgke diacylglycerol kinase, epsilon NM_019505 Dgkg diacylglycerol kinase, gamma NM_138650 Dgkh diacylglycerol kinase, eta XM_358465 Dgki diacylglycerol kinase, iota XM_355752 Dgkq diacylglycerol kinase, theta NM_199011 Dgkz diacylglycerol kinase zeta NM_138306 Dguok NM_013764 Dlg5 discs, large homolog 5 (Drosophila) XM_127605 discs, large (Drosophila) homolog- Dlgap3 NM_198618 associated protein 3 Dlgh1 discs, large homolog 1 (Drosophila) NM_007862 Dlgh2 discs, large homolog 2 (Drosophila) NM_011807 Dlgh3 discs, large homolog 3 (Drosophila) NM_016747 Dlgh4 discs, large homolog 4 (Drosophila) NM_007864 Dmpk dystrophia myotonica-protein kinase NM_032418 DnaJ (Hsp40) homolog, subfamily A, Dnaja2 NM_019794 member 2 DnaJ (Hsp40) homolog, subfamily A, Dnaja4 NM_021422 member 4 DnaJ (Hsp40) homolog, subfamily B, Dnajb1 NM_018808 member 1 DnaJ (Hsp40) homolog, subfamily B, Dnajb10 NM_020266 member 10 DnaJ (Hsp40) homolog, subfamily B, Dnajb12 NM_019965 member 12 DnaJ (Hsp40) homolog, subfamily B, Dnajb3 NM_008299 member 3 DnaJ (Hsp40) homolog, subfamily B, Dnajb5 NM_019874 member 5 DnaJ (Hsp40) homolog, subfamily B, Dnajb6 NM_011847 member 6 DnaJ (Hsp40) homolog, subfamily B, Dnajb8 NM_019964 member 8 DnaJ (Hsp40) homolog, subfamily B, Dnajb9 NM_013760 member 9 DnaJ (Hsp40) homolog, subfamily C, Dnajc1 NM_007869 member 1 DnaJ (Hsp40) homolog, subfamily C, Dnajc2 NM_009583 member 2 DnaJ (Hsp40) homolog, subfamily C, Dnajc3 NM_008929 member 3 DnaJ (Hsp40) homolog, subfamily C, Dnajc5 NM_016775 member 5 DnaJ (Hsp40) homolog, subfamily C, Dnajc7 NM_019795 member 7 Dnclc1 dynein, cytoplasmic, light chain 1 NM_019682 Dnm1l dynamin 1-like NM_152816 Doc2b double C2, beta NM_007873 Dtymk deoxythymidylate kinase NM_023136 Dusp1 dual specificity phosphatase 1 NM_013642 Dusp14 dual specificity phosphatase 14 NM_019819 Dusp2 dual specificity phosphatase 2 NM_010090 Dusp8 dual specificity phosphatase 8 NM_008748 Dyrk1a dual-specificity tyrosine-(Y)- NM_007890

192 V. Supplementary Data

phosphorylation regulated kinase 1a dual-specificity tyrosine-(Y)- Dyrk1b NM_010092 phosphorylation regulated kinase 1b dual-specificity tyrosine-(Y)- Dyrk3 NM_145508 phosphorylation regulated kinase 3 dual-specificity tyrosine-(Y)- Dyrk4 NM_207210 phosphorylation regulated kinase 4 E030030I06Rik RIKEN cDNA E030030I06 gene XM_286230 E030037J05Rik RIKEN cDNA E030037J05 gene NM_177169 E130304F04Rik RIKEN cDNA E130304F04 gene NM_175538 Eef2k eukaryotic elongation factor-2 kinase NM_007908 Efhc1 EF-hand domain (C-terminal) containing 1 XM_129694 Egfr epidermal growth factor receptor NM_007912 eukaryotic translation initiation factor 2 Eif2ak1 NM_013557 alpha kinase 1 eukaryotic translation initiation factor 2 Eif2ak3 NM_010121 alpha kinase 3 eukaryotic translation initiation factor 2 Eif2ak4 NM_013719 alpha kinase 4 Endog endonuclease G NM_007931 Epha1 Eph receptor A1 NM_023580 Epha10 Eph receptor A10 NM_177671 Epha2 Eph receptor A2 NM_010139 Epha3 Eph receptor A3 NM_010140 Epha4 Eph receptor A4 NM_007936 Epha5 Eph receptor A5 NM_007937 Epha6 Eph receptor A6 NM_007938 Epha7 Eph receptor A7 NM_010141 Epha8 Eph receptor A8 NM_007939 Ephb1 Eph receptor B1 NM_173447 Ephb2 Eph receptor B2 NM_010142 Ephb3 Eph receptor B3 NM_010143 Ephb4 Eph receptor B4 NM_010144 Ephb6 Eph receptor B6 NM_007680 v-erb-b2 erythroblastic leukemia viral Erbb2 oncogene homolog 2, neuro/glioblastoma XM_109715 derived oncogene homolog (avian) v-erb-b2 erythroblastic leukemia viral Erbb3 XM_125954 oncogene homolog 3 (avian) v-erb-a erythroblastic leukemia viral Erbb4 XM_136682 oncogene homolog 4 (avian) endoplasmic reticulum (ER) to nucleus Ern1 NM_023913 signalling 1 endoplasmic reticulum (ER) to nucleus Ern2 NM_012016 signalling 2 Etnk1 1 XM_284250 Etnk2 ethanolamine kinase 2 NM_175443 Eya1 eyes absent 1 homolog (Drosophila) NM_010164 Eya2 eyes absent 2 homolog (Drosophila) NM_010165 Eya3 eyes absent 3 homolog (Drosophila) NM_010166 Fastk Fas-activated serine/threonine kinase NM_023229 Fbxw11 F-box and WD-40 domain protein 11 NM_134015 Fbxw8 F-box and WD-40 domain protein 8 NM_172721 Fer1l3 fer-1-like 3, myoferlin (C. elegans) XM_283556 Fer1l4 fer-1-like 4 (C. elegans) XM_110396

193

V. Supplementary Data

fer (fms/fps related) protein kinase, testis Fert2 NM_008000 specific 2 Fes feline sarcoma oncogene NM_010194 Fgfr1 fibroblast growth factor receptor 1 NM_010206 Fgfr2 fibroblast growth factor receptor 2 NM_010207 Fgfr3 fibroblast growth factor receptor 3 NM_008010 Fgfr4 fibroblast growth factor receptor 4 NM_008011 Gardner-Rasheed feline sarcoma viral (Fgr) Fgr NM_010208 oncogene homolog Fkbp1a FK506 binding protein 1a NM_008019 Fkbp8 FK506 binding protein 8 NM_010223 Flt3 FMS-like tyrosine kinase 3 NM_010229 Flt3l FMS-like tyrosine kinase 3 ligand NM_013520 Flt4 FMS-like tyrosine kinase 4 NM_008029 Fn3k fructosamine 3 kinase NM_022014 FK506 binding protein 12-rapamycin Frap1 NM_020009 associated protein 1 Frk fyn-related kinase NM_010237 Frmd6 FERM domain containing 6 NM_028127 Fuk NM_172283 Fyn Fyn proto-oncogene NM_008054 fizzy/cell division cycle 20 related 1 Fzr1 NM_019757 (Drosophila) Gak cyclin G associated kinase XM_132229 Galk1 1 NM_016905 Galk2 galactokinase 2 NM_175154 Gck glucokinase NM_010292 Gcs1 glucosidase 1 NM_020619 Gk2 2 NM_010294 Gm1078 gene model 1078, (NCBI) XM_355840 Gm1079 gene model 1079, (NCBI) XM_355841 Gm1247 gene model 1247, (NCBI) XM_356879 Gm1257 gene model 1257, (NCBI) XM_356951 Gm1280 gene model 1280, (NCBI) XM_357069 Gm1295 gene model 1295, (NCBI) XM_357104 Gm1389 gene model 1389, (NCBI) XM_357542 Gm1390 gene model 1390, (NCBI) XM_357543 Gm1445 gene model 1445, (NCBI) XM_357795 Gm1455 gene model 1455, (NCBI) XM_357849 Gm1464 gene model 1464, (NCBI) XM_357893 Gm162 gene model 162, (NCBI) XM_133316 Gm1757 gene model 1757, (NCBI) XM_358924 Gm1847 gene model 1847, (NCBI) XM_142330 Gm1860 gene model 1860, (NCBI) XM_203222 Gm1872 gene model 1872, (NCBI) XM_354585 Gm1890 gene model 1890, (NCBI) XM_355336 Gm1913 gene model 1913, (NCBI) XM_356690 Gm234 gene model 234, (NCBI) XM_137065 Gm270 gene model 270, (NCBI) XM_138612 Gm272 gene model 272, (NCBI) XM_138614 Gm282 gene model 282, (NCBI) XM_138906 Gm300 gene model 300, (NCBI) XM_139294 Gm318 gene model 318, (NCBI) XM_139919 Gm324 gene model 324, (NCBI) XM_140045

194 V. Supplementary Data

Gm360 gene model 360, (NCBI) XM_141596 Gm489 gene model 489, (NCBI) XM_145693 Gm642 gene model 642, (NCBI) XM_194688 Gm711 gene model 711, (NCBI) NM_198628 Gm936 gene model 936, (NCBI) XM_354996 Gm942 gene model 942, (NCBI) XM_355031 Gmip Gem-interacting protein NM_198101 guanine nucleotide binding protein (G Gnb2l1 NM_008143 protein), beta polypeptide 2 like 1 Gne glucosamine NM_015828 G protein-coupled receptor kinase 2, Gprk2l NM_019497 groucho gene related (Drosophila) Gprk5 G protein-coupled receptor kinase 5 NM_018869 Gprk6 G protein-coupled receptor kinase 6 NM_011938 Grk1 G protein-coupled receptpr kinase 1 NM_011881 Gsg2 germ cell-specific gene 2 NM_010353 Gsk3b glycogen synthase kinase 3 beta NM_019827 GSN gelsolin (amyloidosis, Finnish type) NM_000177 Gucy1a3 1, soluble, alpha 3 NM_021896 Gucy1b2 guanylate cyclase 1, soluble, beta 2 NM_172810 Gucy1b3 guanylate cyclase 1, soluble, beta 3 NM_017469 Gucy2c XM_132928 Gucy2e guanylate cyclase 2e NM_008192 Gucy2f guanylate cyclase 2f XM_142224 Guk1 1 NM_008193 Gyk glycerol kinase NM_008194 Gykl1 glycerol kinase-like 1 NM_010293 Hck hemopoietic cell kinase NM_010407 Hdac6 histone deacetylase 6 NM_010413 Hipk1 homeodomain interacting protein kinase 1 NM_010432 Hipk2 homeodomain interacting protein kinase 2 NM_010433 Hipk3 homeodomain interacting protein kinase 3 NM_010434 Hk1 1 NM_010438 Hk2 hexokinase 2 NM_013820 Hk3 hexokinase 3 XM_127381 Hkdc1 hexokinase domain containing 1 NM_145419 Hoxa10 homeo box A10 NM_008263 Hoxa5 homeo box A5 NM_010453 Hoxa7 homeo box A7 NM_010455 Hoxa9 homeo box A9 NM_010456 Hsf1 heat shock factor 1 NM_008296 Hspa14 heat shock 70kDa protein 14 NM_015765 Hspa1a heat shock protein 1A XM_207062 Hspa2 heat shock protein 2 NM_008301 heat shock 70kD protein 5 (glucose- Hspa5 NM_022310 regulated protein) Hspb1 heat shock protein 1 NM_013560 Hspca heat shock protein 1, alpha NM_010480 Hspcb heat shock protein 1, beta NM_008302 hormonally upregulated Neu-associated Hunk NM_015755 kinase Ide insulin degrading enzyme NM_031156 Igf1r insulin-like growth factor I receptor NM_010513 Ihpk1 inositol hexaphosphate kinase 1 NM_013785

195

V. Supplementary Data

Ikbkb inhibitor of kappaB kinase beta NM_010546 Ikbke inhibitor of kappaB kinase epsilon NM_019777 Ilk integrin linked kinase NM_010562 Insr insulin receptor NM_010568 Insrr insulin receptor-related receptor NM_011832 Ipmk inositol polyphosphate multikinase XM_125641 Irak2 interleukin-1 receptor-associated kinase 2 NM_172161 Irak3 interleukin-1 receptor-associated kinase 3 NM_028679 Irak4 interleukin-1 receptor-associated kinase 4 NM_029926 Itch itchy XM_192925 integrin, alpha 4 (antigen CD49D, alpha 4 ITGA4 NM_000885 subunit of VLA-4 receptor) Itgb1bp3 integrin beta 1 binding protein 3 XM_125745 Itk IL2-inducible T-cell kinase NM_010583 Itpk1 inositol 1,3,4-triphosphate 5/6 kinase NM_172584 Itpka inositol 1,4,5-trisphosphate 3-kinase A NM_146125 Itpkb inositol 1,4,5-trisphosphate 3-kinase B XM_205854 Itpkc inositol 1,4,5-trisphosphate 3-kinase C NM_181593 Itpkc inositol 1,4,5-trisphosphate 3-kinase C NM_181593 Itpr1 inositol 1,4,5-triphosphate receptor 1 NM_010585 Itpr3 inositol 1,4,5-triphosphate receptor 3 NM_080553 Jak1 Janus kinase 1 NM_146145 Jak1 Janus kinase 1 NM_146145 Jak2 Janus kinase 2 NM_008413 Jak3 Janus kinase 3 NM_010589 Kdr kinase insert domain protein receptor NM_010612 Khk ketohexokinase NM_008439 Kit kit oncogene NM_021099 Ksr kinase suppressor of ras NM_013571 LAT linker for activation of T cells NM_014387 Lats1 large tumor supressor XM_194716 Lats2 large tumor suppressor 2 NM_015771 LBP lipopolysaccharide binding protein NM_004139 Lck lymphocyte protein tyrosine kinase NM_010693 Lef1 lymphoid enhancer binding factor 1 NM_010703 Limk1 LIM-domain containing, protein kinase NM_010717 Limk2 LIM motif-containing protein kinase 2 NM_010718 Lmtk2 lemur tyrosine kinase 2 XM_132499 Lmtk3 lemur tyrosine kinase 3 XM_356032 LOC209203 similar to heat shock protein 1, beta XM_142222 LOC210619 similar to RP3-330M21.4 XM_140038 similar to Dysferlin (Dystrophy associated LOC211430 XM_136730 fer-1 like protein) (Fer-1 like protein 1) LOC216178 similar to TAK1 (TGF-beta-activated kinase) XM_125802 LOC225264 similar to 3 XM_140199 LOC227885 similar to heat shock protein 1, beta XM_140982 LOC229005 similar to Pim2 protein XM_130753 similar to Nucleoside diphosphate kinase B LOC229879 XM_143595 (NDK B) (NDP kinase B) (P18) LOC232619 similar to hypothetical protein XM_145207 LOC233024 similar to protein kinase C zeta XM_124895 similar to pyruvate kinase (EC 2.7.1.40) LOC237016 XM_142088 isozyme M2 - rat LOC238119 similar to Pyruvate kinase 3 XM_137993

196 V. Supplementary Data

LOC238564 similar to myosin light chain kinase XM_111421 LOC238678 similar to Methylmalonic aciduria type A XM_138664 LOC241051 similar to PHD finger protein 19 XM_136726 LOC241572 similar to Pyruvate kinase 3 XM_141269 LOC241864 similar to SNF related kinase XM_143053 LOC245068 similar to putative protein kinase XM_142402 similar to Casein kinase II, alpha 1 LOC245355 XM_141642 polypeptide LOC279333 similar to TOPK XM_205529 similar to Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing beta LOC329248 polypeptide (Phosphoinositide 3-Kinase- XM_283638 C2-beta) (PtdIns-3-kinase C2 beta) (PI3K- C2beta) (C2-PI3K) similar to CDC42-binding protein kinase LOC329302 XM_283676 alpha LOC333050 similar to kinase suppressor of ras 2 XM_285897 LOC381164 similar to Pgk1 protein XM_355086 LOC381390 similar to serine/threonine kinase XM_355352 LOC381936 similar to Ser/Thr protein kinase PAR-1A XM_355960 LOC381937 similar to Ser/Thr protein kinase PAR-1A XM_355961 similar to novel protein similar to LOC383041 XM_356816 vertebrate otoferlin (OTOF) LOC383956 similar to putative protein kinase XM_357348 similar to Rho-associated coiled-coil LOC385049 XM_358017 forming kinase 1 LOC385092 similar to putative protein kinase XM_358047 LOC546214 similar to putative protein kinase XM_142616 LOC546236 similar to putative protein kinase XM_135656 Lrrk2 leucine-rich repeat kinase 2 NM_025730 Ltk leukocyte tyrosine kinase NM_206941 Yamaguchi sarcoma viral (v-yes-1) Lyn NM_010747 oncogene homolog mannose-6-phosphate receptor (cation M6PR NM_002355 dependent) mannose-6-phosphate receptor binding M6PRBP1 NM_005817 protein 1 Mamdc1 MAM domain containing 1 NM_207010 Map2k1 mitogen activated protein kinase kinase 1 NM_008927 Map2k2 mitogen activated protein kinase kinase 2 NM_023138 Map2k3 mitogen activated protein kinase kinase 3 NM_008928 Map2k4 mitogen activated protein kinase kinase 4 NM_009157 Map2k5 mitogen activated protein kinase kinase 5 NM_011840 Map2k6 mitogen activated protein kinase kinase 6 NM_011943 Map2k7 mitogen activated protein kinase kinase 7 NM_011944 mitogen activated protein kinase kinase Map3k1 NM_011945 kinase 1 mitogen activated protein kinase kinase Map3k10 XM_194344 kinase 10 mitogen activated protein kinase kinase Map3k11 NM_022012 kinase 11 mitogen activated protein kinase kinase Map3k12 NM_009582 kinase 12 mitogen-activated protein kinase kinase Map3k14 NM_016896 kinase 14

197

V. Supplementary Data

mitogen activated protein kinase kinase Map3k2 NM_011946 kinase 2 mitogen activated protein kinase kinase Map3k3 NM_011947 kinase 3 mitogen activated protein kinase kinase Map3k4 NM_011948 kinase 4 mitogen activated protein kinase kinase Map3k5 NM_008580 kinase 5 mitogen-activated protein kinase kinase Map3k6 NM_016693 kinase 6 mitogen activated protein kinase kinase Map3k7 NM_172688 kinase 7 mitogen activated protein kinase kinase Map3k8 NM_007746 kinase 8 mitogen-activated protein kinase kinase Map3k9 NM_177395 kinase 9 mitogen activated protein kinase kinase Map4k1 NM_008279 kinase kinase 1 mitogen activated protein kinase kinase Map4k2 NM_009006 kinase kinase 2 mitogen-activated protein kinase kinase Map4k3 XM_128800 kinase kinase 3 mitogen-activated protein kinase kinase Map4k4 NM_008696 kinase kinase 4 mitogen-activated protein kinase kinase Map4k5 NM_024275 kinase kinase 5 Mapk1 mitogen activated protein kinase 1 NM_011949 Mapk10 mitogen activated protein kinase 10 NM_009158 Mapk11 mitogen-activated protein kinase 11 NM_011161 Mapk12 mitogen-activated protein kinase 12 NM_013871 Mapk13 mitogen activated protein kinase 13 NM_011950 Mapk14 mitogen activated protein kinase 14 NM_011951 Mapk15 mitogen-activated protein kinase 15 NM_177922 Mapk3 mitogen activated protein kinase 3 NM_011952 Mapk4 mitogen-activated protein kinase 4 NM_172632 Mapk6 mitogen-activated protein kinase 6 NM_015806 Mapk7 mitogen activated protein kinase 7 NM_011841 Mapk8 mitogen activated protein kinase 8 NM_016700 mitogen activated protein kinase 8 Mapk8ip1 NM_011162 interacting protein 1 Mapk9 mitogen activated protein kinase 9 NM_016961 Mapkapk2 MAP kinase-activated protein kinase 2 NM_008551 mitogen-activated protein kinase-activated Mapkapk3 NM_178907 protein kinase 3 Mapkapk5 MAP kinase-activated protein kinase 5 NM_010765 macrophage receptor with collagenous MARCO NM_006770 structure MAP/microtubule affinity-regulating kinase Mark1 NM_145515 1 MAP/microtubule affinity-regulating kinase Mark2 NM_007928 2 MAP/microtubule affinity-regulating kinase Mark3 NM_022801 3 MAP/microtubule affinity-regulating kinase Mark4 NM_172279 4 Mast2 microtubule associated serine/threonine NM_008641

198 V. Supplementary Data

kinase 2 microtubule associated serine/threonine Mast3 NM_199308 kinase 3 microtubule associated serine/threonine Mast4 XM_283179 kinase family member 4 microtubule associated serine/threonine Mastl NM_025979 kinase-like Matk megakaryocyte-associated tyrosine kinase NM_010768 Meis1 myeloid ecotropic viral integration site 1 NM_010789 Melk maternal embryonic leucine zipper kinase NM_010790 Mep1b meprin 1 beta NM_008586 Mertk c-mer proto-oncogene tyrosine kinase NM_008587 Met met proto-oncogene NM_008591 MGC102419 similar to mNori-2p XM_355368 Ras-GTPase-activating protein SH3-domain MGI:1351465 NM_013716 binding protein Mink1 misshapen-like kinase 1 (zebrafish) NM_016713 MAP kinase-interacting serine/threonine Mknk1 NM_021461 kinase 1 MAP kinase-interacting serine/threonine Mknk2 NM_021462 kinase 2 Mlkl mixed lineage kinase domain-like XM_356104 Morc microrchidia NM_010816 Morc3 microrchidia 3 XM_128334 Mos Moloney sarcoma oncogene NM_020021 Mpp1 membrane protein, palmitoylated NM_008621 membrane protein, palmitoylated 2 Mpp2 NM_016695 (MAGUK p55 subfamily member 2) membrane protein, palmitoylated 3 Mpp3 NM_007863 (MAGUK p55 subfamily member 3) membrane protein, palmitoylated 4 Mpp4 NM_145143 (MAGUK p55 subfamily member 4) membrane protein, palmitoylated 5 Mpp5 NM_019579 (MAGUK p55 subfamily member 5) membrane protein, palmitoylated 6 Mpp6 NM_019939 (MAGUK p55 subfamily member 6) MRC1 mannose receptor, C type 1 NM_002438 MRC2 mannose receptor, C type 2 NM_006039 meiotic recombination 11 homolog A (S. Mre11a NM_018736 cerevisiae) MSR1 macrophage scavenger receptor 1 NM_002445 macrophage stimulating 1 receptor (c-met- Mst1r NM_009074 related tyrosine kinase) Mtmr2 myotubularin related protein 2 NM_023858 Mtmr3 myotubularin related protein 3 NM_028860 Mtmr7 myotubularin related protein 7 NM_019433 Muc3 mucin 3, intestinal XM_355711 Mulk multiple lipid kinase NM_023538 Musk muscle, skeletal, receptor tyrosine kinase NM_010944 Mvk NM_023556 Mylk myosin, light polypeptide kinase NM_139300 myosin, light polypeptide kinase 2, skeletal Mylk2 XM_130630 muscle Myo3a myosin IIIA NM_148413 Myo3b myosin IIIB XM_194023

199

V. Supplementary Data

Nadk NAD kinase NM_138671 Nbn nibrin NM_013752 non-catalytic region of tyrosine kinase Nck1 NM_010878 adaptor protein 1 neural precursor cell expressed, Nedd8 NM_008683 developmentally down-regulated gene 8 NIMA (never in mitosis gene a)-related Nek11 NM_172461 expressed kinase 11 NIMA (never in mitosis gene a)-related Nek2 NM_010892 expressed kinase 2 NIMA (never in mitosis gene a)-related Nek3 NM_011848 expressed kinase 3 NIMA (never in mitosis gene a)-related Nek4 NM_011849 expressed kinase 4 NIMA (never in mitosis gene a)-related Nek5 NM_177898 expressed kinase 5 NIMA (never in mitosis gene a)-related Nek6 NM_021606 expressed kinase 6 NIMA (never in mitosis gene a)-related Nek7 NM_021605 expressed kinase 7 NIMA (never in mitosis gene a)-related Nek8 NM_080849 expressed kinase 8 NIMA (never in mitosis gene a)-related Nek9 NM_145138 expressed kinase 9 nuclear factor of kappa light chain gene Nfkb1 NM_008689 enhancer in B-cells 1, p105 Nlk nemo like kinase NM_008702 Nme1 expressed in non-metastatic cells 1, protein NM_008704 Nme2 expressed in non-metastatic cells 2, protein NM_008705 Nme3 expressed in non-metastatic cells 3 NM_019730 Nme4 expressed in non-metastatic cells 4, protein NM_019731 Nme5 expressed in non-metastatic cells 5 NM_080637 Nme6 expressed in non-metastatic cells 6, protein NM_018757 Nme7 non-metastatic cells 7, protein expressed in NM_138314 Npr1 natriuretic peptide receptor 1 NM_008727 Npr2 natriuretic peptide receptor 2 NM_173788 Nrbp nuclear receptor binding protein NM_147201 Nrbp2 nuclear receptor binding protein 2 NM_144847 Nrk Nik related kinase NM_013724 Nrp1 neuropilin 1 NM_008737 Nrp2 neuropilin 2 NM_010939 neurotrophic tyrosine kinase, receptor, type Ntrk1 XM_283871 1 neurotrophic tyrosine kinase, receptor, type Ntrk2 NM_008745 2 neurotrophic tyrosine kinase, receptor, type Ntrk3 NM_008746 3 Nuak1 ZNUAK family, SNF1-like kinase, 1 XM_196007 Nuak2 NUAK family, SNF1-like kinase, 2 NM_028778 Olfr1047 olfactory receptor 1047 NM_147012 Olfr1226 olfactory receptor 1226 NM_146967 Olfr1228 olfactory receptor 1228 NM_146971 Olfr1233 olfactory receptor 1233 NM_146972 Olfr1234 olfactory receptor 1234 NM_146973 Olfr1239 olfactory receptor 1239 NM_146970

200 V. Supplementary Data

Olfr1242 olfactory receptor 1242 NM_146968 Olfr1243 olfactory receptor 1243 NM_146969 Olfr1255 olfactory receptor 1255 NM_146977 Olfr1256 olfactory receptor 1256 NM_146983 Olfr1258 olfactory receptor 1258 NM_146978 Olfr1260 olfactory receptor 1260 NM_146981 Olfr1262 olfactory receptor 1262 NM_146974 Olfr1264 olfactory receptor 1264 NM_021368 Olfr1272 olfactory receptor 1272 NM_146980 Olfr140 olfactory receptor 140 NM_020515 Olfr1509 olfactory receptor 1509 NM_020514 Olfr32 olfactory receptor 32 NM_010980 Oxsr1 oxidative-stress responsive 1 XM_135264 Pak1 p21 (CDKN1A)-activated kinase 1 NM_011035 Pak2 p21 (CDKN1A)-activated kinase 2 NM_177326 Pak3 p21 (CDKN1A)-activated kinase 3 NM_008778 Pak4 p21 (CDKN1A)-activated kinase 4 NM_027470 Pak6 p21 (CDKN1A)-activated kinase 6 XM_111790 Pak7 p21 (CDKN1A)-activated kinase 7 NM_172858 Pank1 1 NM_023792 pantothenate kinase 2 (Hallervorden-Spatz Pank2 NM_153501 syndrome) Pank3 pantothenate kinase 3 NM_145962 Pank4 pantothenate kinase 4 NM_172990 3'-phosphoadenosine 5'-phosphosulfate Papss1 NM_011863 synthase 1 3'-phosphoadenosine 5'-phosphosulfate Papss2 NM_011864 synthase 2 PAS domain containing serine/threonine Pask NM_080850 kinase Pbk PDZ binding kinase NM_023209 Pbx1 pre B-cell leukemia transcription factor 1 NM_008783 Pcgf2 polycomb group ring finger 2 NM_009545 phosphoenolpyruvate carboxykinase 1, Pck1 NM_011044 cytosolic Pctk1 PCTAIRE-motif protein kinase 1 NM_011049 Pctk2 PCTAIRE-motif protein kinase 2 NM_146239 Pctk3 PCTAIRE-motif protein kinase 3 NM_008795 Pdia3 protein disulfide associated 3 NM_007952 Pdik1l PDLIM1 interacting kinase 1 like NM_146156 pyruvate dehydrogenase kinase, isoenzyme Pdk2 NM_133667 2 pyruvate dehydrogenase kinase, isoenzyme Pdk3 NM_145630 3 pyruvate dehydrogenase kinase, isoenzyme Pdk4 NM_013743 4 PDLIM5 PDZ and LIM domain 5 NM_006457 3-phosphoinositide dependent protein Pdpk1 NM_011062 kinase-1 Pdxk pyridoxal (pyridoxine, vitamin B6) kinase NM_172134 Pdzk8 PDZ domain containing 8 XM_140761 6-phosphofructo-2-kinase/fructose-2,6- Pfkfb1 XM_284750 biphosphatase 1 6-phosphofructo-2-kinase/fructose-2,6- Pfkfb2 NM_008825 biphosphatase 2

201

V. Supplementary Data

6-phosphofructo-2-kinase/fructose-2,6- Pfkfb3 NM_172976 biphosphatase 3 6-phosphofructo-2-kinase/fructose-2,6- Pfkfb4 NM_173019 biphosphatase 4 Pfkl , liver, B-type NM_008826 Pfkm phosphofructokinase, muscle NM_021514 Pftk1 PFTAIRE protein kinase 1 NM_011074 Pgk1 1 NM_008828 Pgk2 phosphoglycerate kinase 2 NM_031190 Phc1 polyhomeotic-like 1 (Drosophila) NM_007905 Phka1 kinase alpha 1 NM_008832 Phka2 phosphorylase kinase alpha 2 NM_172783 Phkb phosphorylase kinase beta NM_199446 Phkg1 phosphorylase kinase gamma 1 NM_011079 Phkg2 phosphorylase kinase, gamma 2 (testis) NM_026888 Pi4k2a phosphatidylinositol 4-kinase type 2 alpha NM_145501 Pi4k2b phosphatidylinositol 4-kinase type 2 beta NM_025951 phosphatidylinositol 3-kinase, C2 domain Pik3c2a NM_011083 containing, alpha polypeptide phosphatidylinositol 3-kinase, C2 domain Pik3c2g NM_011084 containing, gamma polypeptide Pik3c3 phosphoinositide-3-kinase, class 3 NM_181414 phosphatidylinositol 3-kinase, catalytic, Pik3ca NM_008839 alpha polypeptide phosphatidylinositol 3-kinase, catalytic, Pik3cb NM_029094 beta polypeptide phosphatidylinositol 3-kinase catalytic Pik3cd NM_008840 delta polypeptide phosphoinositide-3-kinase, catalytic, Pik3cg NM_020272 gamma polypeptide phosphatidylinositol 3-kinase, regulatory Pik3r2 NM_008841 subunit, polypeptide 2 (p85 beta) phosphatidylinositol 3 kinase, regulatory Pik3r3 NM_181585 subunit, polypeptide 3 (p55) phosphatidylinositol 3 kinase, regulatory Pik3r4 XM_135116 subunit, polypeptide 4, p150 phosphatidylinositol 4-kinase, catalytic, Pik4cb NM_175356 beta polypeptide Pim1 proviral integration site 1 NM_008842 Pim2 proviral integration site 2 NM_138606 Pim3 proviral integration site 3 NM_145478 protein (peptidyl-prolyl cis/trans isomerase) Pin1 NM_023371 NIMA-interacting 1 Pink1 PTEN induced putative kinase 1 NM_026880 phosphatidylinositol-4-phosphate 5-kinase, Pip5k1a NM_008846 type 1 alpha phosphatidylinositol-4-phosphate 5-kinase, Pip5k1b NM_008847 type 1 beta phosphatidylinositol-4-phosphate 5-kinase, Pip5k1c NM_008844 type 1 gamma phosphatidylinositol-4-phosphate 5-kinase, Pip5k2a NM_008845 type II, alpha phosphatidylinositol-4-phosphate 5-kinase, Pip5k2b NM_054051 type II, beta phosphatidylinositol-4-phosphate 5-kinase, Pip5k2c NM_054097 type II, gamma

202 V. Supplementary Data

phosphatidylinositol-3- Pip5k3 phosphate/phosphatidylinositol 5-kinase, NM_011086 type III phosphatidylinositol-4-phosphate 5-kinase- Pip5kl1 NM_198191 like 1 Pkia protein kinase inhibitor, alpha NM_008862 Pklr pyruvate kinase liver and red blood cell NM_013631 Pkm2 pyruvate kinase, muscle NM_011099 protein kinase, membrane associated Pkmyt1 NM_023058 tyrosine/threonine 1 Pkn1 protein kinase N1 NM_177262 Pkn2 protein kinase N2 NM_178654 Pkn3 protein kinase N3 NM_153805 Plcg1 phospholipase C, gamma 1 NM_021280 Plcl1 phospholipase C-like 1 XM_129785 Plcl2 phospholipase C-like 2 NM_013880 Plk1 polo-like kinase 1 (Drosophila) NM_011121 Plk2 polo-like kinase 2 (Drosophila) NM_152804 Plk3 polo-like kinase 3 (Drosophila) NM_013807 Plk4 polo-like kinase 4 (Drosophila) NM_011495 Pln phospholamban NM_023129 Pmvk NM_026784 pregnancy upregulated non-ubiquitously Pnck NM_012040 expressed CaM kinase Pnkp polynucleotide kinase 3'- phosphatase NM_021549 protein tyrosine phosphatase, receptor- Ppfibp2 type, F interacting protein, binding protein NM_008905 2 Ppid peptidylprolyl isomerase D (cyclophilin D) NM_026352 protein phosphatase 1, catalytic subunit, Ppp1ca NM_031868 alpha isoform protein phosphatase 2a, catalytic subunit, Ppp2cb NM_017374 beta isoform protein phosphatase 2 (formerly 2A), Ppp2r1a NM_016891 regulatory subunit A (PR 65), alpha isoform protein phosphatase 3, catalytic subunit, Ppp3cc NM_008915 gamma isoform protein phosphatase 3, regulatory subunit Ppp3r1 NM_024459 B, alpha isoform (calcineurin B, type I) protein kinase, AMP-activated, alpha 1 Prkaa1 XM_139298 catalytic subunit protein kinase, AMP-activated, alpha 2 Prkaa2 XM_131633 catalytic subunit protein kinase, AMP-activated, beta 1 non- Prkab1 NM_031869 catalytic subunit protein kinase, AMP-activated, beta 2 non- Prkab2 NM_182997 catalytic subunit protein kinase, cAMP dependent, catalytic, Prkaca NM_008854 alpha protein kinase, cAMP dependent, catalytic, Prkaca-ps1 XM_205338 alpha pseudogene 1 protein kinase, cAMP dependent, catalytic, Prkacb NM_011100 beta protein kinase, AMP-activated, gamma 1 Prkag1 NM_016781 non-catalytic subunit Prkag3 protein kinase, AMP-activated, gamma 3 NM_153744

203

V. Supplementary Data

non-catatlytic subunit protein kinase, cAMP dependent Prkar1a NM_021880 regulatory, type I, alpha protein kinase, cAMP dependent Prkar1b NM_008923 regulatory, type I beta protein kinase, cAMP dependent Prkar2a NM_008924 regulatory, type II alpha protein kinase, cAMP dependent Prkar2b NM_011158 regulatory, type II beta Prkca protein kinase C, alpha NM_011101 Prkcb1 protein kinase C, beta 1 NM_008855 Prkcc protein kinase C, gamma NM_011102 Prkcd protein kinase C, delta NM_011103 Prkce protein kinase C, epsilon NM_011104 Prkch protein kinase C, eta NM_008856 Prkci protein kinase C, iota NM_008857 Prkcm protein kinase C, mu NM_008858 Prkcn protein kinase C, nu NM_029239 Prkcq protein kinase C, theta NM_178075 Prkcsh protein kinase C substrate 80K-H NM_008925 Prkcz protein kinase C, zeta NM_008860 Prkd2 protein kinase D2 NM_178900 protein kinase, DNA activated, catalytic Prkdc NM_011159 polypeptide Prkg1 protein kinase, cGMP-dependent, type I NM_011160 Prkg2 protein kinase, cGMP-dependent, type II NM_008926 protein kinase, interferon-inducible double Prkr NM_011163 stranded RNA dependent protein kinase, interferon inducible double Prkra NM_011871 stranded RNA dependent activator Prkwnk1 protein kinase, lysine deficient 1 NM_198703 Prkwnk3 protein kinase, lysine deficient 3 XM_205148 Prkwnk4 protein kinase, lysine deficient 4 NM_175638 Prkx protein kinase, X-linked NM_016979 Prnd prion protein dublet NM_023043 PRP4 pre-mRNA processing factor 4 Prpf4b NM_013830 homolog B (yeast) phosphoribosyl pyrophosphate synthetase Prps1 NM_021463 1 phosphoribosyl pyrophosphate synthetase Prps2 NM_026662 2 Prss7 protease, serine, 7 (enterokinase) NM_008941 Pskh1 protein serine kinase H1 NM_173432 Pten phosphatase and tensin homolog NM_008960 Ptk2 PTK2 protein tyrosine kinase 2 NM_007982 Ptk2b PTK2 protein tyrosine kinase 2 beta NM_172498 Ptk6 PTK6 protein tyrosine kinase 6 NM_009184 Ptk7 PTK7 protein tyrosine kinase 7 NM_175168 Ptk9 protein tyrosine kinase 9 NM_008971 protein tyrosine kinase 9-like (A6-related Ptk9l NM_011876 protein) Ptp4a1 protein tyrosine phosphatase 4a1 NM_011200 Ptp4a2 protein tyrosine phosphatase 4a2 NM_008974 Ptp4a3 protein tyrosine phosphatase 4a3 NM_008975 Ptpla protein tyrosine phosphatase-like (proline NM_013935

204 V. Supplementary Data

instead of catalytic arginine), member a protein tyrosine phosphatase-like (proline Ptplb NM_023587 instead of catalytic arginine), member b protein tyrosine phosphatase, non-receptor Ptpn1 NM_011201 type 1 protein tyrosine phosphatase, non-receptor Ptpn11 NM_011202 type 11 protein tyrosine phosphatase, non-receptor Ptpn12 NM_011203 type 12 protein tyrosine phosphatase, non-receptor Ptpn13 NM_011204 type 13 protein tyrosine phosphatase, non-receptor Ptpn14 NM_008976 type 14 protein tyrosine phosphatase, non-receptor Ptpn18 NM_011206 type 18 protein tyrosine phosphatase, non-receptor Ptpn2 NM_008977 type 2 protein tyrosine phosphatase, non-receptor Ptpn20 NM_008978 type 20 protein tyrosine phosphatase, non-receptor Ptpn21 NM_011877 type 21 protein tyrosine phosphatase, non-receptor Ptpn22 NM_008979 type 22 (lymphoid) protein tyrosine phosphatase, non-receptor Ptpn4 NM_019933 type 4 protein tyrosine phosphatase, non-receptor Ptpn5 NM_013643 type 5 protein tyrosine phosphatase, non-receptor Ptpn6 NM_013545 type 6 protein tyrosine phosphatase, non-receptor Ptpn7 NM_177081 type 7 protein tyrosine phosphatase, non-receptor Ptpn9 NM_019651 type 9 protein tyrosine phosphatase, non-receptor Ptpns1 NM_007547 type substrate 1 protein tyrosine phosphatase, receptor Ptpra NM_008980 type, A protein tyrosine phosphatase, receptor Ptprb NM_029928 type, B protein tyrosine phosphatase, receptor Ptprc NM_011210 type, C protein tyrosine phosphatase, receptor Ptprcap NM_016933 type, C polypeptide-associated protein protein tyrosine phosphatase, receptor Ptpre NM_011212 type, E protein tyrosine phosphatase, receptor Ptprf NM_011213 type, F protein tyrosine phosphatase, receptor Ptprg NM_008981 type, G protein tyrosine phosphatase, receptor Ptprj NM_008982 type, J protein tyrosine phosphatase, receptor Ptprk NM_008983 type, K protein tyrosine phosphatase, receptor Ptprm NM_008984 type, M protein tyrosine phosphatase, receptor Ptprn NM_008985 type, N

205

V. Supplementary Data

protein tyrosine phosphatase, receptor Ptprn2 NM_011215 type, N polypeptide 2 protein tyrosine phosphatase, receptor Ptpro NM_011216 type, O protein tyrosine phosphatase, receptor Ptprr NM_011217 type, R protein tyrosine phosphatase, receptor Ptprs NM_011218 type, S protein tyrosine phosphatase, receptor Ptprt NM_021464 type, T protein tyrosine phosphatase, receptor Ptpru NM_011214 type, U protein tyrosine phosphatase, receptor Ptprv NM_007955 type, V PTX1 PTX1 protein NM_016570 PX domain containing serine/threonine Pxk NM_145458 kinase Rab11fip1 RAB11 family interacting protein 1 (class I) XM_134088 Racgap1 Rac GTPase-activating protein 1 NM_012025 Rad51 RAD51 homolog (S. cerevisiae) NM_011234 Rad9 RAD9 homolog (S. pombe) NM_011237 Raf1 v-raf-1 leukemia viral oncogene 1 NM_029780 Rage renal tumor antigen NM_011973 Rasgrp3 RAS, guanyl releasing protein 3 NM_207246 Ret ret proto-oncogene NM_009050 RFWD2 ring finger and WD repeat domain 2 NM_001001740 Riok1 RIO kinase 1 (yeast) NM_024242 Riok2 RIO kinase 2 (yeast) NM_025934 Riok3 RIO kinase 3 (yeast) NM_024182 receptor (TNFRSF)-interacting serine- Ripk1 NM_009068 threonine kinase 1 receptor (TNFRSF)-interacting serine- Ripk2 NM_138952 threonine kinase 2 receptor-interacting serine-threonine kinase Ripk3 NM_019955 3 receptor-interacting serine-threonine kinase Ripk4 NM_023663 4 ribonuclease L (2', 5'-oligoisoadenylate Rnasel NM_011882 synthetase-dependent) RNA and 5'- Rngtt NM_011884 phosphatase Rho-associated coiled-coil forming kinase Rock1 NM_009071 1 Rho-associated coiled-coil forming kinase Rock2 NM_009072 2 receptor tyrosine kinase-like orphan Ror1 NM_013845 receptor 1 receptor tyrosine kinase-like orphan Ror2 NM_013846 receptor 2 Ros1 Ros1 proto-oncogene NM_011282 Rp26 retinitis pigmentosa 26 XM_149165 Rps6ka1 ribosomal protein S6 kinase polypeptide 1 NM_009097 Rps6ka2 ribosomal protein S6 kinase, polypeptide 2 NM_011299 Rps6ka3 ribosomal protein S6 kinase polypeptide 3 NM_148945 Rps6ka4 ribosomal protein S6 kinase, polypeptide 4 NM_019924 Rps6ka6 ribosomal protein S6 kinase polypeptide 6 NM_025949

206 V. Supplementary Data

Rps6kb1 ribosomal protein S6 kinase, polypeptide 1 NM_028259 Rps6kb2 ribosomal protein S6 kinase, polypeptide 2 NM_021485 Rps6kl1 ribosomal protein S6 kinase-like 1 NM_146244 Ryk receptor-like tyrosine kinase NM_013649 Scyl1 SCY1-like 1 (S. cerevisiae) NM_023912 Scyl2 SCY1-like 2 (S. cerevisiae) NM_198021 Scyl3 SCY1-like 3 (S. cerevisiae) NM_028776 serine (or cysteine) peptidase inhibitor, Serpinh1 NM_009825 clade H, member 1 Sfpi1 SFFV proviral integration 1 NM_011355 Sgk serum/glucocorticoid regulated kinase NM_011361 Sgk2 serum/glucocorticoid regulated kinase 2 NM_013731 Sgk3 serum/glucocorticoid regulated kinase 3 NM_133220 Skp1a S-phase kinase-associated protein 1A NM_011543 Slk STE20-like kinase (yeast) NM_009289 Smok2 sperm motility kinase 2 XM_135514 SMAD specific E3 ubiquitin protein Smurf2 XM_126673 2 Snf1lk SNF1-like kinase NM_010831 Snf1lk2 SNF1-like kinase 2 NM_178710 Snrk SNF related kinase NM_133741 Spata5 spermatogenesis associated 5 NM_021343 Sphk1 1 NM_011451 Sphk2 sphingosine kinase 2 NM_020011 Src Rous sarcoma oncogene NM_009271 src-related kinase lacking C-terminal Srms regulatory tyrosine and N-terminal NM_011481 myristylation sites serine/arginine-rich protein specific kinase Srpk1 NM_016795 1 serine/arginine-rich protein specific kinase Srpk2 NM_009274 2 signal transducer and activator of Stat5a NM_011488 transcription 5A signal transducer and activator of Stat5b NM_011489 transcription 5B Stk10 serine/threonine kinase 10 NM_009288 Stk11 serine/threonine kinase 11 NM_011492 Stk16 serine/threonine kinase 16 NM_011494 serine/threonine kinase 17b (apoptosis- Stk17b NM_133810 inducing) Stk19 serine/threonine kinase 19 NM_019442 serine/threonine kinase 24 (STE20 Stk24 NM_145465 homolog, yeast) Stk25 serine/threonine kinase 25 (yeast) NM_021537 Stk31 serine threonine kinase 31 NM_029916 Stk32a serine/threonine kinase 32A NM_178749 Stk32b serine/threonine kinase 32B NM_022416 Stk32c serine/threonine kinase 32C NM_021302 Stk33 serine/threonine kinase 33 XM_358897 Stk35 serine/threonine kinase 35 NM_183262 serine/threonine kinase 36 (fused homolog, Stk36 NM_175031 Drosophila) Stk38 serine/threonine kinase 38 NM_134115 Stk38l serine/threonine kinase 38 like NM_172734

207

V. Supplementary Data

serine/threonine kinase 39, STE20/SPS1 Stk39 NM_016866 homolog (yeast) Stk4 serine/threonine kinase 4 NM_021420 Stk40 serine/threonine kinase 40 NM_028800 STIP1 homology and U-Box containing Stub1 NM_019719 protein 1 Styk1 serine/threonine/tyrosine kinase 1 NM_172891 phosphoserine/threonine/tyrosine Styx NM_019637 interaction protein Syk spleen tyrosine kinase NM_011518 Syt3 synaptotagmin III NM_016663 Taok2 TAO kinase 2 XM_355941 Tbk1 TANK-binding kinase 1 NM_019786 Tcf7 transcription factor 7, T-cell specific NM_009331 cytoplasmic tyrosine kinase, Dscr28C Tec NM_013689 related (Drosophila) endothelial-specific receptor tyrosine Tek NM_013690 kinase tensin like C1 domain-containing Tenc1 NM_153533 phosphatase Tesk1 testis specific protein kinase 1 NM_011571 Tesk2 testis-specific kinase 2 NM_146151 Tex14 testis expressed gene 14 NM_031386 Tgfbr1 transforming growth factor, beta receptor I NM_009370 Tgfbr2 transforming growth factor, beta receptor II NM_009371 transforming growth factor, beta receptor Tgfbrap1 XM_129857 associated protein 1 Tgm2 transglutaminase 2, C polypeptide NM_009373 Tie1 tyrosine kinase receptor 1 NM_011587 Tk1 1 NM_009387 Tk2 thymidine kinase 2, mitochondrial NM_021028 Tlk2 tousled-like kinase 2 (Arabidopsis) NM_011903 Tnik TRAF2 and NCK interacting kinase XM_130797 Tnk1 tyrosine kinase, non-receptor, 1 NM_031880 Tnk2 tyrosine kinase, non-receptor, 2 NM_016788 Tor1a torsin family 1, member A (torsin A) NM_144884 Tpk1 thiamin pyrophosphokinase NM_013861 Trib1 tribbles homolog 1 (Drosophila) NM_144549 Trib2 tribbles homolog 2 (Drosophila) NM_144551 Trib3 tribbles homolog 3 (Drosophila) NM_175093 Trip13 thyroid hormone receptor interactor 13 XM_127444 Trp53rk TP53 regulating kinase NM_023815 Trp63 transformation related protein 63 NM_011641 Trp73 transformation related protein 73 NM_011642 transient receptor potential cation channel, Trpm6 NM_153417 subfamily M, member 6 transient receptor potential cation channel, Trpm7 NM_021450 subfamily M, member 7 Tssk1 testis-specific serine kinase 1 NM_009435 Tssk2 testis-specific serine kinase 2 NM_009436 Tssk3 testis-specific serine kinase 3 NM_021479 Tssk3 testis-specific serine kinase 3 NM_080442 Tssk4 testis-specific serine kinase 4 NM_027673 Tssk5 testis-specific serine kinase 5 NM_183099

208 V. Supplementary Data

Tssk6 testis-specific serine kinase 6 NM_032004 Ttbk1 tau tubulin kinase 1 NM_080788 Ttk Ttk protein kinase NM_009445 Txk TXK tyrosine kinase NM_013698 family LPS-inducible Tyki NM_020557 member Tyro3 TYRO3 protein tyrosine kinase 3 NM_019392 Ube1x ubiquitin-activating enzyme E1, Chr X NM_009457 Ube2j1 ubiquitin-conjugating enzyme E2, J1 NM_019586 ubiquitination factor E4B, UFD2 homolog Ube4b NM_022022 (S. cerevisiae) Ubxd4 UBX domain containing 4 NM_145441 Ubxd5 UBX domain containing 5 NM_026257 Uchl1 ubiquitin carboxy-terminal L1 NM_011670 Uck1 uridine-cytidine kinase 1 NM_011675 Uck2 uridine-cytidine kinase 2 NM_030724 Uckl1 uridine-cytidine kinase 1-like 1 NM_026765 Ugp2 UDP-glucose pyrophosphorylase 2 NM_139297 Uhmk1 U2AF homology motif (UHM) kinase 1 NM_010633 Ulk1 Unc-51 like kinase 1 (C. elegans) NM_009469 Ulk2 Unc-51 like kinase 2 (C. elegans) NM_013881 Unc13a unc-13 homolog A (C. elegans) XM_356087 Unc13c unc-13 homolog C (C. elegans) XM_146948 Unc13d unc-13 homolog D (C. elegans) XM_126670 UNK UNK NM_177357 UNK UNK XM_110361 UNK UNK XM_125105 UNK UNK XM_126461 UNK UNK XM_127694 UNK UNK XM_130894 UNK UNK XM_131934 UNK UNK XM_134994 UNK UNK XM_136679 UNK UNK XM_138790 UNK UNK XM_139182 UNK UNK XM_142163 UNK UNK XM_142409 UNK UNK XM_144303 UNK UNK XM_145594 UNK UNK XM_156269 UNK UNK XM_193575 UNK UNK XM_195367 UNK UNK XM_195404 UNK UNK XM_289801 UNK UNK XM_354997 UNK UNK XM_355003 UNK UNK XM_355088 UNK UNK XM_355107 UNK UNK XM_355257 UNK UNK XM_355351 UNK UNK XM_355401 UNK UNK XM_355556 UNK UNK XM_355649

209

V. Supplementary Data

UNK UNK XM_355671 UNK UNK XM_355672 UNK UNK XM_355962 UNK UNK XM_356004 UNK UNK XM_356027 UNK UNK XM_356052 UNK UNK XM_356182 UNK UNK XM_356581 UNK UNK XM_356582 UNK UNK XM_356631 UNK UNK XM_356664 UNK UNK XM_356672 UNK UNK XM_356672 UNK UNK XM_356726 UNK UNK XM_356727 UNK UNK XM_356937 UNK UNK XM_357073 UNK UNK XM_357110 UNK UNK XM_357261 UNK UNK XM_357278 UNK UNK XM_357434 UNK UNK XM_357516 UNK UNK XM_357527 UNK UNK XM_357546 UNK UNK XM_357547 UNK UNK XM_357598 UNK UNK XM_357655 UNK UNK XM_357668 UNK UNK XM_357700 UNK UNK XM_357784 UNK UNK XM_357926 UNK UNK XM_358135 UNK UNK XM_358261 UNK UNK XM_358804 UNK UNK XM_359157 UNK UNK XM_359221 UNK UNK XM_359299 Vcp valosin containing protein NM_009503 Vdac1 voltage-dependent anion channel 1 NM_011694 Vdac2 voltage-dependent anion channel 2 NM_011695 Vdac3 voltage-dependent anion channel 3 NM_011696 Vrk1 vaccinia related kinase 1 NM_011705 Vrk2 vaccinia related kinase 2 NM_027260 Vrk3 vaccinia related kinase 3 NM_133945 Wasf1 WASP family 1 NM_031877 Wee1 wee 1 homolog (S. pombe) NM_009516 Wnk2 WNK lysine deficient protein kinase 2 XM_127323 WW domain containing E3 ubiquitin Wwp1 XM_130163 protein ligase 1 X99384 cDNA sequence X99384 NM_013753 Xbp1 X-box binding protein 1 NM_013842 Xylb homolog (H. influenzae) XM_135223 Yes1 Yamaguchi sarcoma viral (v-yes) oncogene NM_009535

210 V. Supplementary Data

homolog 1 Yeast Sps1/Ste20-related kinase 4 (S. Ysk4 XM_136210 cerevisiae) tyrosine 3-monooxygenase/tryptophan 5- Ywhae monooxygenase activation protein, epsilon NM_009536 polypeptide Zap70 zeta-chain (TCR) associated protein kinase NM_009539

UNK - Unknown

Table S2 – Gene list of vesicular traffic screened subset.

Gene Gene Description NM number adaptor protein complex AP- Ap2m1 NM_009679 2, mu1 Arcn1 archain 1 NM_145985 Arf1 ADPribosylation factor 1 NM_007476 B2m Beta 2 microglobulin NM_009735 blocked early in transport 1 Bet1 NM_009748 homolog (S. cerevisiae) blocked early in transport 1 Bet1l NM_018742 homolog (S. cerevisiae)like BCL2/adenovirus E1B Bnip1 NM_172149 interacting protein 1 Cav1 caveolin, caveolae protein 1 NM_007616 Cav2 caveolin 2 NM_016900 Cav3 caveolin 3 NM_007617 Cd1d1 CD1d1 antigen NM_007639 clathrin, light polypeptide Clta NM_016760 (Lca) clathrin, light polypeptide Cltb NM_028870 (Lcb) clathrin, heavy polypeptide Cltc NM_001003908 (Hc) coatomer protein complex Copa NM_009938 subunit alpha coatomer protein complex, Copb1 NM_033370 subunit beta 1 coatomer protein complex, Copb2 NM_015827 subunit beta 2 (beta prime) coatomer protein complex, Cope NM_021538 subunit epsilon coatomer protein complex, Copg NM_201244 subunit gamma coatomer protein complex, Copg2 NM_017478 subunit gamma 2 coatomer protein complex, Copz1 NM_019817 subunit zeta 1 coatomer protein complex, Copz2 NM_019877 subunit zeta 2 carnitine Crot NM_023733 Ooctanoyltransferase cytochrome b245, beta Cybb NM_007807 polypeptide Degs1 degenerative spermatocyte NM_007853

211

V. Supplementary Data

homolog 1 (Drosophila) Dnm1 dynamin 1 NM_010065 Dnm2 dynamin 2 NM_007871 Dnm3 dynamin 3 NM_172646 golgi SNAP receptor complex Gosr1 NM_016810 member 1 golgi SNAP receptor complex Gosr2 NM_019650 member 2 lectin, galactose binding, Lgals3 NM_010705 soluble 3 lectin, galactose binding, Lgals9 NM_010708 soluble 9 myosin VIIA and Rab Myrip NM_144557 interacting protein RAB1, member RAS Rab1 NM_008996 oncogene family RAB10, member RAS Rab10 NM_016676 oncogene family RAB11a, member RAS Rab11a NM_017382 oncogene family RAB11B, member RAS Rab11b NM_008997 oncogene family RAB11 family interacting Rab11fip1 XM_134088 protein 1 (class I) RAB11 family interacting Rab11fip2 NM_001033172 protein 2 (class I) RAB11 family interacting Rab11fip3 XM_484616 protein 3 (class II) RAB11 family interacting Rab11fip4 NM_175543 protein 4 (class II) RAB11 family interacting Rab11fip5 NM_001003955 protein 5 (class I) RAB13, member RAS Rab13 NM_026677 oncogene family RAB14, member RAS Rab14 NM_026697 oncogene family RAB15, member RAS Rab15 NM_134050 oncogene family RAB17, member RAS Rab17 NM_008998 oncogene family RAB18, member RAS Rab18 NM_011225 oncogene family RAB19, member RAS Rab19 NM_011226 oncogene family RAB1B, member RAS Rab1b NM_029576 oncogene family RAB20, member RAS Rab20 NM_011227 oncogene family RAB21, member RAS Rab21 NM_024454 oncogene family RAB22A, member RAS Rab22a NM_024436 oncogene family RAB23, member RAS Rab23 NM_008999 oncogene family RAB24, member RAS Rab24 NM_009000 oncogene family Rab25 RAB25, member RAS NM_016899

212 V. Supplementary Data

oncogene family RAB27A, member RAS Rab27a NM_023635 oncogene family RAB27b, member RAS Rab27b NM_030554 oncogene family RAB28, member RAS Rab28 NM_027295 oncogene family RAB2A, member RAS Rab2a NM_021518 oncogene family RAB2B, member RAS Rab2b NM_172601 oncogene family RAB30, member RAS Rab30 NM_029494 oncogene family RAB31, member RAS Rab31 NM_133685 oncogene family RAB32, member RAS Rab32 NM_026405 oncogene family RAB33A, member of RAS Rab33a NM_011228 oncogene family RAB33B, member of RAS Rab33b NM_016858 oncogene family RAB34, member of RAS Rab34 NM_033475 oncogene family RAB35, member of RAS Rab35 NM_198163 oncogene family RAB36, member of RAS Rab36 NM_029781 oncogene family RAB37, member of RAS Rab37 NM_021411 oncogene family RAB38, member of RAS Rab38 NM_028238 oncogene family RAB39, member of RAS Rab39 NM_175562 oncogene family RAB39B, member RAS Rab39b NM_175122 oncogene family RAB3A, member RAS Rab3a NM_009001 oncogene family RAB3B, member RAS Rab3b NM_023537 oncogene family RAB3C, member RAS Rab3c NM_023852 oncogene family RAB3D, member RAS Rab3d NM_031874 oncogene family RAB3 GTPase activating Rab3gap1 NM_178690 protein subunit 1 RAB3A interacting protein Rab3il1 NM_144538 (rabin3)like 1 Rab3ip RAB3A interacting protein NM_001003950 Rab40b, member RAS Rab40b NM_139147 oncogene family Rab40c, member RAS Rab40c NM_139154 oncogene family RAB43, member RAS Rab43 NM_133717 oncogene family RAB4A, member RAS Rab4a NM_009003 oncogene family Rab4b RAB4B, member RAS NM_029391

213

V. Supplementary Data

oncogene family RAB5A, member RAS Rab5a NM_025887 oncogene family RAB5B, member RAS Rab5b NM_177411 oncogene family RAB5C, member RAS Rab5c NM_024456 oncogene family RAB6, member RAS Rab6 NM_024287 oncogene family RAB6B, member RAS Rab6b NM_173781 oncogene family Rab6ip1 Rab6 interacting protein 1 NM_021494 RAB7, member RAS Rab7 NM_009005 oncogene family RAB7, member RAS Rab7l1 NM_144875 oncogene familylike 1 RAB8A, member RAS Rab8a NM_023126 oncogene family RAB8B, member RAS Rab8b NM_173413 oncogene family RAB9, member RAS Rab9 NM_019773 oncogene family RAB9B, member RAS Rab9b NM_176971 oncogene family rabaptin, RAB GTPase Rabep1 NM_019400 binding effector protein 1 Rab9 effector protein with Rabepk NM_145522 kelch motifs RAB GTPase activating Rabgap1 NM_146121 protein 1 RAB GTPase activating Rabgap1l NM_013862 protein 1like RAB guanine nucleotide Rabgef1 NM_019983 exchange factor (GEF) 1 Rab geranylgeranyl Rabggta NM_019519 , a subunit RAB geranylgeranyl Rabggtb NM_011231 transferase, b subunit Rabif RAB interacting factor NM_145510 RAB, member of RAS Rabl2a NM_026817 oncogene familylike 2A RAB, member of RAS Rabl4 NM_025931 oncogene familylike 4 Rin1 Ras and Rab interactor 1 NM_145495 Rin2 Ras and Rab interactor 2 NM_028724 Rin3 Ras and Rab interactor 3 NM_177620 Rph3a rabphilin 3A NM_011286 rabphilin 3Alike (without C2 Rph3al NM_029548 domains) Sec13l1 SEC13 homolog (S. cerevisiae) NM_024206 SEC22 vesicle trafficking Sec22a NM_133704 proteinlike A (S. cerevisiae) SEC22 vesicle trafficking Sec22b protein homolog B (S. NM_011342 cerevisiae) SEC22 vesicle trafficking Sec22c NM_178677 proteinlike C (S. cerevisiae)

214 V. Supplementary Data

Sec23a SEC23A (S. cerevisiae) NM_009147 Sec23b SEC23B (S. cerevisiae) NM_019787 Sec23ip Sec23 interacting protein NM_001029982 SEC24 related gene family, Sec24a NM_175255 member A (S. cerevisiae) SEC24 related gene family, Sec24b XM_131192 member B (S. cerevisiae) SEC24 related gene family, Sec24c NM_172596 member C (S. cerevisiae) SEC24 related gene family, Sec24d NM_027135 member D (S. cerevisiae) Sec61g SEC61, gamma subunit NM_011343 synaptosomalassociated Snap23 NM_009222 protein 23 synaptosomalassociated Snap25 NM_011428 protein 25 synaptosomalassociated Snap29 NM_023348 protein 29 synaptosomalassociated Snap91 NM_013669 protein 91 Stx12 syntaxin 12 NM_133887 Stx16 syntaxin 16 NM_172675 Stx17 syntaxin 17 NM_026343 Stx18 syntaxin 18 NM_026959 Stx1b1 syntaxin 1B NM_019560 Stx1b2 syntaxin 1B NM_024414 Stx3 syntaxin 3 NM_001025307 Stx4a syntaxin 4A (placental) NM_009294 Stx5a syntaxin 5A NM_019829 Stx6 syntaxin 6 NM_021433 Stx7 syntaxin 7 NM_016797 Stx8 syntaxin 8 NM_018768 Stxbp1 syntaxin binding protein 1 NM_009295 Stxbp2 syntaxin binding protein 2 NM_011503 Stxbp3a syntaxin binding protein 3A NM_011504 Stxbp4 syntaxin binding protein 4 NM_011505 Stxbp5l syntaxin binding protein 5like NM_172440 syntaxin binding protein 6 Stxbp6 NM_144552 (amisyn) Vesicle associated membrane Sybl1 NM_011515 protein 7 unconventional SNARE in the Use1 NM_029768 ER 1 homolog (S. cerevisiae) Vesicle associated membrane Vamp1 NM_009496 protein 1 Vesicle associated membrane Vamp3 NM_009498 protein 3 Vesicle associated membrane Vamp4 NM_016796 protein 4 Vesicle associated membrane Vamp5 NM_016872 protein 5 vesicle transport through Vti1a interaction with tSNAREs NM_016862 homolog 1A (yeast) vesicle transport through Vti1b interaction with tSNAREs 1B NM_016800 homolog

215

V. Supplementary Data

Ykt6 YKT6 homolog (S. Cerevisiae) NM_019661

216

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217 References

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