Supplemental Figure 1: Immunoelectron microscopy of ribeye on the harvested sucrose pellet from the gradient centrifugation shown in multiple panels.

Supplemental Figure 2: Immunoelectron microscopy of VAMP2 on the harvested 200-400 mM sucrose interface sample shown in multiple panels.

Supplemental Figure 3: A. Western blots indicate the immunoprecipitation of ribeye and CtBP2 with the CtBP2 . Also coimmunoprecipitation of

CtBP1, , 9H, and α- is shown. B. Western blots indicate the immunoprecipitation of only ribeye with the AD antibody and the coimmunoprecipitation of PRPF39 is indicated.

Supplemental Figure 4. Colocalization of ribeye with various presynaptic . The labeling of individual proteins is presented in grayscale and merged panels are depicted in color. Double-labeling with ribeye-specific antiserum reveals the localization with respect to synaptic ribbons of SNARE proteins such as syntaxin 1 (A-C), SNAP25 (D-F), VAMP2 (G-I), syntaxin 6 (J-L), SNAP23 (M-O), VAMP7 (P-R), VAP-33 (S-U); SNARE dissociation molecules such as α-SNAP, β-SNAP (V-X), NSF (Y-A′); hair-cell specific proteins such as glutamate receptors 2 and 3 (GluR2 and GluR3) (B′-D′), vGluT3 (E′-G′), hair-cell specific Ca2+ channel Cav1.3 (H′-J′), calcium sensor otoferlin (K′-M′); and other synaptic proteins such as rabphilin (N′-P′), munc 18 (Q′-S′), and synapsin (T′-V′).

Supplemental Figure 5. Colocalization of ribeye with endocytotic and vesicle- trafficking proteins. The labeling of individual proteins is presented in grayscale and merged panels are depicted in color. Double-labeling with ribeye-specific antiserum reveals the localization of the endocytic proteins clathrin (A-C), (D-F), SCAMP1 (G-I) and endophilin (J-L) and of the trafficking proteins

Sec13 (M-O), β-COP (P-R), VCP (S-U), and GAPDH (V-X) with respect to synaptic ribbons.

Supplemental Figure 6. Colocalization of ribeye with cytoskeletal proteins. The labeling of individual proteins is presented in grayscale and merged panels are depicted in color. Double-labeling with ribeye-specific antiserum reveals the localization of the cytoskeletal proteins α-tubulin (A-C), spectrin (D-F), MYH9 (G-I), β- (J-L), NF200 (M-O), and KIF3A (P-R) with respect to synaptic ribbons.

Supplemental Table 1: Listing of and antisera used in immunoblotting and immunocytochemical experiments.

Supplemental Tables 2-7: Identification of cochlear proteins from sucrose gradients. The isolated proteins are tabulated in alphabetical order. For each , the accession number and the protein score defining the total fragment ions matching score (MS/MS matches only) is shown. Protein scores are derived from ion scores as a non-probabilistic basis for ranking protein hits. The ion score is -10·log(P), in which P is the probability that the observed match is a random event. We used stringent criteria for protein identification: a protein was designated as a “hit” only if it matched at least two distinct peptides with an ion score of at least 40. A single-peptide match was considered if the peptide had a good tandem mass spectrum and matched only a single protein. Because we used the non-redundant NCBI (NCBInr) Chordata database to search the tandem mass-spectrometric data, the accession numbers represent different species; when data from multiple species are used, that with the highest score is used. Also shown are the protein's mass, the peptide matches that define the total number of peptides matched to that protein, the protein coverage giving the percentage of peptide sequences matched to that protein, and the isoelectric point (PI).

Supplemental Table 2: Identification of proteins from the sucrose pellet in the cochlea.

Supplemental Table 3: Identification of proteins from the sucrose pellet in the retina.

Supplemental Table 4: Identification of proteins from the harvested sucrose gradients between the 200-400 mM interface from cochlear material.

Supplemental Table 5: Identification of proteins from the harvested sucrose gradients between the 400-600 mM interface from cochlear material.

Supplemental Table 6: Identification of proteins from the harvested sucrose gradients between the 600-800 mM interface from cochlear material.

Supplemental Table 7: Identification of proteins from the 47,000 x g pellet fraction from cochlear material. EM negative staining of the sucrose pellet fraction with the AD antibody indicating ribeye staining

A B

C D

Scale bar: 100 nm EM negative staining of the vesicle fraction between the 200-400 mM sucrose layers using VAMP2 antibody A B

C D

E F

Scale bar: 100 nm A. Coimmunoprecipitation with CtBP2 antibody: experiment I and experiment II (results in Table 2)

eads P l b kDa kDa Ab flowthPreolulegthSupernaFtelonwt througChontro CTBP2 I Ab flowPtehlrleotuSguhpernaFtleonwtthroEulguhtion1Elution2Elution3Beads 120 120 100 ribeye 100 ribeye 80 80 60 60 50 50 CtBP2 CtBP2

50 CtBP1 40 myosin 9H 220

120 50 50 40 actin spectrin 30 40 20 30

60 50

40

B. Coimmunoprecipitation with AD antibody (Table 3 results)

l o l t h r o n nt tr o n co kDa h as Pellet SupernateFlowthroWug Elution1 Elution2 Beads Elution cBeads

120 Ribeye 100 80

60 50 IgG CtBP2

120 100 80 PRPF39

60 IgG 50 A ribeye B syntaxin 1 C Merge B’ ribeye C’ GluR 2/3 D’ Merge Phalloidin Phalloidin

D ribeye E SNAP25 F Merge Phalloidin

E’ ribeye F’ vGlut3 G’ Merge Phalloidin

G ribeye H VAMP2 I Merge Phalloidin

H’ ribeye I’ Cav1.3 J’ Merge J ribeye K syntaxin 6 L Merge Phalloidin Phalloidin

K’ ribeye L’ Otoferlin M’ Merge M ribeye N SNAP23 O Merge Phalloidin Phalloidin

P ribeye Q VAMP7 R Merge Phalloidin

N’ ribeye O’ rabphilin P’ Merge Phalloidin S ribeye T VAP-33 U Merge Phalloidin

V ribeye W X Merge Phalloidin Q’ ribeye R’ munc18 S’ Merge Phalloidin

Y ribeye Z NSF A’ Merge Phalloidin

T’ ribeye U’ synapsin V’ Merge Phalloidin A ribeye B clathrin C Merge M ribeye N Sec13 O Merge Phalloidin Phalloidin

P ribeye Q R Merge Phalloidin D ribeye E dynamin F Merge Phalloidin

S ribeye T VCP U Merge Phalloidin G ribeye H SCAMP1 I Merge Phalloidin

J endophilin K ribeye L Merge V ribeye W GAPDH X Merge Phalloidin Phalloidin A B ribeye C Merge Phalloidin

D spectrin E CtBP2 F Merge Phalloidin

G myosin H9 H CtBP2 I Merge Phalloidin

J ribeye K L Merge Phalloidin

M NF200 N CtBP2 O Merge Phalloidin

P KIF3A Q CtBP2 R Merge Phalloidin Supplemental Table 1. List of antibodies and antisera.

Antibodies Company and catalog number Concentrations Immunoblot Immunocytochemistry Otoferlin (R), HCS1 J.T. Corwin’s Laboratory NA 1:500 bassoon (M) Abcam ab76065 1:1000 1:500 NIPSNAP1 (R) Abcam ab67302 NA 1:200 SNAP25 (R) Abcam ab24737 1:1000 NA SNAP25 (m) Synaptic Systems 111 011 NA 1:200 VAMP1 (R) Abcam ab3346 1:2000 1:250 VAMP7 (M) Abcam ab36195 NA 1:100 clathrin heavy chain (M) Affinity Bioreagents MA1-065 1:500 1:250 VAMP2 (R) Assay Designs VAS-SV006F 1:2000 NA VAMP2 (M) Stressgen VAMSV014E NA 1:250 CASK (M) BD Transduction Laboratories 610782 1:500 NA CtBP1 (M) BD Transduction Laboratories 612042 1:2000 1:500 CtBP2 (M) BD Transduction Laboratories 612044 1:1000 1:500 dynamin (M) BD Transduction Laboratories 610246 1:1000 1:500 munc13 (M) BD Transduction Laboratories 610998 1:1000 NA munc18 (M) BD Transduction Laboratories 610337 1:1000 1:100 N-cadherin BD Transduction Laboratories 610920 1:2500 NA Rab3 (M) BD Transduction Laboratories 610380 1:2500 1:250 Rabphilin (M) BD Transduction Laboratories 610509 NA 1:250 RIM1 (M) BD Transduction Laboratories 610906 1:500 NA SCAMP1 (M) BD Transduction Laboratories 612087 NA 1:100 synapsin 1 (R) BD Transduction Laboratories 611392 1:10,000 NA Synapsin 1 (R) Hudspeth Laboratory NA 1:200 synaptotagmin1 (M) BD Transduction Laboratories 610434 1:500 NA syntaxin 4 (M) BD Transduction Laboratories 610439 1:10,000 NA syntaxin 6 (M) BD Transduction Laboratories 610635 1:2500 1:200 tomosyn (M) BD Transduction Laboratories 611297 1:500 NA VAP-33 (M) BD Transduction Laboratories 612180 1:2000 1:100 VCP97 (M) BD Transduction Laboratories 612182 NA 1:250 β-Catenin (M) BD Transduction Laboratories 610154 1:500 1:500 CaMKII (R) Cell Signalling 3361S NA 1:50 Complexin 1/2 (R) Chemicon International AB9288 1:1000 NA gluR 2 and 3 (R) Chemicon International AB 1506 NA 1:100 SV2 (M) Developmental Hybridoma Bank 1:1000 NA GAPDH (M) Millipore MAB374 1:1000 1:1000 GFAP (M) Novus Biologicals NB 300-141 1:1000 NA Sec13 (M) Novus Biologicals H00006396-A01 NA 1:100 β-COP (R) Pierce Biotechnology PA1-061 NA 1:100 CaBP4 (G) Santa Cruz Biotechnology sc-28096 1:500 1:500 synaptophysin 1 (R) Santa Cruz Biotechnology sc-9116 1:500 1:500 α-SNAP, β-SNAP (M) Santa Cruz Biotechnology sc-48349 1:250 1:100 actin (R) Sigma A 2066 1:500 1:250 KIF3A (R) Sigma K 3513 1:1000 1:200 Myosin H9 (R) Sigma M 8064 NA 1:500 NF160 (M) Sigma N 5264 1:1000 NA NF200 (R) Sigma N 4142 1:1000 1:250 NF68 (M) Sigma N 5139 1:1000 NA NSF (M) Sigma N 6038 1:2000 1:500 SNAP23 (R) Sigma Prestige Andtibodies HPA001214 1:2000 1:200 syntaxin 1 (M) Sigma S 0664 1:2000 1: 250 Synaptophysin (M) Sigma S 5768 Syntaxin 7 (R) Sigma S 4819 1:1000 NA α-tubulin (M) Sigma T 6074 1:2000 1:500 γ-tubulin (M) Sigma T 3559 1:10,000 NA Spectrin (M) Sigma Immunochemicals S1390 NA 1:200 PRPF39 (R) Sigma Prestige Antibodies HPA001176 NA 1:100 CSP (R) Stressgen VAP-SV003 1:5000 NA ERC2 (R) Synaptic Systems 143 103 1:1000 NA Piccolo (R) Synaptic Systems 142 002 1:2000 1:200 RIM2 (R) Synaptic Systems 140 103 1:1000 NA synaptojanin (R) Synaptic Systems 145 003 1:1000 NA VAMP3 (R) Synaptic Systems 104 103 1:2000 1:200 Cav1.3 (R) Teresa Nicholson’s Laboratory NA 1:500 vGLUT3 (R) Teresa Nicholson’s Laboratory NA 1:250 Ribeye (R) Hudspeth Laboratory 1:1000 1:250 endophilin (R) Invitrogen 36-3400 1:2000 NA endophilin (R) Harvey McMahon Laboratory NA 1:100

M, mouse; R, rabbit; G, goat; NA, not applicable Supplemental Table 2

Protein description Accession number Protein score Protein mass Protein matches Protein coverage Isoelectric point

Aconitase 1, soluble [Gallus gallus] gi|72535134 43 98639 2 2.9 6.95 Aconitase 2, mitochondrial [Gallus gallus] gi|45383738 83 86535 3 3.9 8.05 Actin beta [Gallus gallus] gi|63018 2713 42080 166 56.5 5.29 Actin cytoplasmic [Lethenteron japonicum] gi|13699190 2225 42137 138 56.4 5.3 Actin-gamma like protein [Mus musculus] gi|6425087 883 44029 50 40.7 5.11 Actin-related protein gi|381964 59 42659 2 6.4 6.35 Actin, muscle-type (A2) gi|3121741 756 42521 45 36 5.12 , alpha 4 [Gallus gallus] gi|45384104 124 104712 6 6.2 5.13 Adenosine triphosphatase isoform 2 [Gallus gallus] gi|118082377 453 135386 27 14.1 5.76 ADP-ribosylation factor-like 8A [Homo sapiens] gi|20270343 78 21630 2 7.5 7.63 ADP-ribosylation factor-like 8B [Danio rerio] gi|45387563 106 21708 5 13.4 8.65 ADP/ATP 2 ( 25 member 5) gi|113459 266 33102 13 18.8 9.76 Aflatoxin aldehyde reductase [Gallus gallus] gi|118101125 149 36943 4 9.5 6.76 AHNAK nucleoprotein, partial [Gallus gallus] gi|118129464 103 54492 10 16.9 5.19 Albumin [Gallus gallus] gi|45383974 194 71868 10 20 5.51 Aldolase A [Homo sapiens] gi|28614 59 39706 2 5.8 8.34 Aldolase B, fructose-bisphosphate [Gallus gallus] gi|157951672 144 39670 6 12.1 8.81 Aldolase C gi|226855 205 39023 6 20.1 5.79 Aldose reductase [Gallus gallus] gi|50729042 72 36014 6 15.5 7.14 puromycin sensitive [Gallus gallus] gi|118102937 65 96723 3 4.7 5.09 Annexin 11 (CAP-50) [Gallus gallus] gi|61098342 174 39012 9 18.7 8.34 Annexin 2 [Gallus gallus] gi|45382533 574 38901 37 57.2 6.92 Annexin 4 1 [Equus caballus] gi|149727504 370 36272 15 10 5.72 Annexin 5 gi|62738641 572 36159 66 53.8 5.61 Annexin 6 [Gallus gallus] gi|50982399 2892 75579 126 66.8 5.57 Annexin 7 gi|50749404 113 49587 6 8.7 5.71 Annexin 8, VAC beta [Gallus gallus] gi|50749462 1162 36938 44 47.7 5.24 AP-1 complex subunit gamma-1 gi|113349 54 92147 2 1.3 6.36 AP-2, adaptor-related protein complex 2, beta 1 subunit isoform b [Homo sapiens]gi|4557469 97 105398 3 3.8 5.22 Apolipoprotein A-I precursor gi|211146 74 30672 2 5.3 5.97 Apolipoprotein B-100 [Equus caballus] gi|149728117 39 521258 2 0.3 6.53 Apoptotic chromatin condensation inducer 1a [Danio rerio] gi|125806373 46 226296 2 0.5 6.04 Arl3-Gdp [Gallus gallus] gi|118097362 50 24040 2 7 6.71 ARP3 actin-related protein 3 homolog [Homo sapiens] gi|5031573 40 47797 1 5.3 5.61 Aspartate Aminotransferase gi|809192 107 46003 5 18.5 8.26 Attachment region binding protein [Gallus gallus] gi|2388805 39 33620 2 9.9 10.65 Beta-galactoside-binding lectin 16kDa gi|211258 55 13228 2 21.4 4.78 Brain abundant, membrane attached signal protein 1 [Gallus gallus] gi|45383878 51 25423 1 5.7 4.66 BRI3 binding protein [Gallus gallus] gi|92110029 108 26810 2 8 8.97 BTB (POZ) domain containing 14A isoform 2 [Rattus norvegicus] gi|34853069 46 63811 2 1.9 5.73 Calbindin 1, 28kDa [Gallus gallus] gi|45382893 331 30376 17 33.2 4.72 Calcium ATPase (hPMCA4) [Gallus gallus] gi|118102576 295 134378 20 11 5.64 Calcium binding protein [Gallus gallus] gi|50736185 72 20879 2 6.2 4.97 Calcium binding protein P22 [Homo sapiens] gi|6005731 97 22442 3 11.8 4.98 Calcium channel subunit isoform I alpha 2 delta I [Homo sapiens] gi|2781441 47 123181 1 1.8 5.22 Calcium/calmodulin-dependent protein kinase (CaM kinase) II beta [Bos taurus] gi|78369262 38 61185 1 4.4 6.89 [Gallus gallus] gi|71895293 453 68465 19 18.5 4.42 Calpain small subunit [Gallus gallus] gi|2506056 84 24014 2 14 5.05 Calponin 3, acidic [Danio rerio] gi|41054309 41 36915 2 4.3 5.71 Calreticulin [Gallus gallus] gi|44969651 184 47079 15 22.8 4.41 Carbonyl reductase 1 [Gallus gallus] gi|71895267 94 30520 4 10.9 8.5 D [Gallus gallus] gi|50758260 110 151876 5 4.3 5.67 Carotene-9,10-monooxygenase, partial [Ornithorhynchus anatinus] gi|149480289 45 21339 2 4.3 8.39 Casein kinase 1, alpha 1-like [Homo sapiens] gi|21624639 63 39275 2 4.7 9.47 Caspase 5 [Macaca mulatta] gi|109108505 44 45357 4 4.1 8.76 Catechol O methyl [Gallus gallus] gi|50756245 266 30111 12 29.8 6.21 Catenin (cadherin-associated protein), delta 1 [Gallus gallus] gi|118091411 37 103693 1 1.6 6.36 Catenin, alpha 3 isoform 4 [Canis familiaris] gi|73952714 45 101942 1 2.1 6.02 CC chemokine SCYA117 [Danio rerio] gi|125854923 43 9647 2 9.4 8.46 Ccomplement component 4 binding protein, alpha chain precursor [Gallus gallus] gi|45382791 94 50174 4 7.8 5.87 cell division cycle 48 [Paralichthys olivaceus] gi|146448775 97 89949 8 9.1 5.19 CENP-F kinetochore protein gi|924601 54 370674 3 0.4 5.03 CGI-109 protein [Homo sapiens] gi|4929687 84 24680 5 8.8 6.21 Chaperonin containing TCP1, subunit 2 (beta) [Gallus gallus] gi|60302718 169 57737 6 16.1 5.89 Chaperonin containing TCP1, subunit 6A (zeta 1) [Gallus gallus] gi|57525300 180 58008 2 9.4 6.36 20 open reading frame 3 [Gallus gallus] gi|57525135 71 46314 3 6 5.89 Chromosome 6 open reading frame 152 [Equus caballus] gi|149722755 41 80635 3 1.7 8.38 Clathrin heavy chain 1 [Gallus gallus] gi|124339781 1868 193256 91 31.6 5.52 Claudin 1 [Gallus gallus] gi|61889131 92 23011 4 10.4 8.85 Claudin 3 [Gallus gallus] gi|46049089 76 23645 2 9.8 8.02 Coagulation factor C homolog, cochlin (Limulus polyphemus) [Gallus gallus] gi|45384390 72 60016 5 6.4 8.61 Coatomer protein complex, subunit alpha [Gallus gallus] gi|71897175 100 140060 9 9.2 7.53 Coatomer subunit beta~ (Beta~-coat protein) (Beta~-COP) (p102) gi|544075 65 103153 1 2.1 5.15 Coiled-coil-helix-coiled-coil-helix domain containing 2 [Mus musculus] gi|18079334 55 15879 1 8.5 9.78 Copine III [Homo sapiens] gi|4503015 45 60947 1 3 5.6 Creatine kinase brain gi|6573489 3382 42998 193 67.6 5.93 Cystatin C [Gallus gallus] gi|45382805 59 15562 2 12.2 7.6 Cysteine and glycine-rich protein 2 (Cysteine-rich protein 2) (CRP2) gi|461908 143 21809 5 25.3 9.03 Cytochrome b-5 reductase [Gallus gallus] gi|50729140 121 34295 8 18.3 8.7 Cytochrome b5 gi|226450 108 15450 3 22.8 4.9 Cytosckeletal associated protein 4 gi|118082813 54 66169 3 6.6 5.64 Cytosolic NADP-dependent isocitrate dehydrogenase [Gallus gallus] gi|118093509 188 46972 7 12.8 8.02 Deleted in liver cancer 1 [Ornithorhynchus anatinus] gi|149637790 64 46846 2 2.5 6.13 [Gallus gallus] gi|45382979 152 18920 7 21.2 7.52 Dihydropyrimidinase-like 3 [Gallus gallus] gi|45383183 44 62428 3 8.9 6.25 Dipeptidylpeptidase IV [Gallus gallus] gi|71895185 56 86916 2 3.3 5.67 DNA-dependent protein kinase 70 kda DNA-binding subunit [Bos taurus] gi|76673262 36 70241 2 1.5 6.38 DnaJ (Hsp40) homolog, subfamily B, member 14 [Gallus gallus] gi|71897321 42 16316 5 7.3 9.11 Double substrate-specificity short chain dehydrogenase/reductase 2 [Gallus gallus]gi|50748322 110 36502 6 15 8.88 1 [Gallus gallus] gi|71897355 39 136336 1 1.4 6.15 , cytoplasmic, heavy polypeptide 1 [Gallus gallus] gi|118092179 454 532495 26 6 6.16 [Macaca mulatta] gi|109071677 39 509332 2 0.3 9.8 Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor Tu) (EF-Tu) gi|3122072 393 50467 21 27.7 9.1 Elongation factor 2 (EF-2) gi|119168 98 96304 5 6.1 6.31 Endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1 [Gallus gallus] gi|118097331 62 33072 3 14.5 6.25 Enolase 1 [Gallus gallus] gi|46048768 1252 47617 49 38.5 6.17 Enolase alpha (2-phospho-D-glycerate hydro-) (Tau-crystallin) gi|119338 1111 47609 45 31.1 6.37 Enolase gamma gi|182118 100 44568 5 23 4.94 ETO/MTG8-related protein ETO-2 [Mus musculus] gi|2723941 44 69070 2 1.3 7.15 Excision repair cross-complementing rodent repair deficiency, complementation groupgi|4557563 3 [Homo sapiens]55 90019 8 1.2 6.83 Fanconi anemia-associated protein, 24 kDa [Homo sapiens] gi|22748623 55 24053 4 2.8 9.28 FAT tumor suppressor homolog 1, partial [Ornithorhynchus anatinus] gi|149454157 42 247101 2 0.4 4.77 Fatty acid binding protein 3 [Gallus gallus] gi|71894843 54 14807 2 19.5 5.92 B, beta (actin binding protein 278) [Gallus gallus] gi|71896431 80 278493 2 1.3 5.61 Flavin containing monooxygenase 6 [Gallus gallus] gi|45383027 85 61095 5 6.6 8.29 Four and a half LIM domains 3 [Rattus norvegicus] gi|157818687 41 33742 2 6.3 5.67 Gap junction protein, beta 6 [Gallus gallus] gi|45384376 57 31530 4 14.8 8.84 [Gallus gallus] gi|45384386 339 86120 13 15.4 5.93 Glucose phosphate [Gallus gallus] gi|57524920 470 62405 19 19.9 7.4 Glucose-regulated protein 78kDa [Oncorhynchus mykiss] gi|60223019 981 69907 49 33.3 5.02 Glutathione S-transferase [Gallus gallus] gi|50729056 185 17330 9 26.5 9.67 Glyceraldehyde-3-phosphate dehydrogenase gi|211797 5887 35989 218 55.6 8.71 Glycoprotein receptor gp330/megalin [Gallus gallus] gi|118093662 214 534908 7 1.8 4.9 Grb10 interacting GYF protein 1 [Mus musculus] gi|33943105 43 116464 13 0.7 5.32 GRP94 [Ornithorhynchus anatinus] gi|149637905 580 93693 31 23.2 4.84 GTP-binding protein gi|550062 335 23720 12 30.7 6.08 Guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptidegi|45382313 2 [Gallus gallus]183 41121 10 18.9 5.43 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (Transducin betagi|3023838 chain 1) (XGbeta1)329 38161 7 9.7 5.6 H(+)/K(+) ATPase subunit alpha gi|20137385 291 116245 19 5.3 5.37 H+ transporting ATP synthase, mitochondrial F1 complex, alpha subunit [Gallus gallus]gi|45383566 512 60263 19 28 9.29 H+ transporting ATPase, mitochondrial F1 complex, beta subunit [Gallus gallus] gi|71897237 115 56650 8 15.6 5.59 Heat shock protein 108 kDa gi|211945 211 91835 12 13.6 4.86 Heat shock protein 70 [Gallus gallus] gi|30962014 704 70098 42 33.4 5.66 Heat shock protein 90kDa beta (Grp94), member 1 [Gallus gallus] gi|45383562 639 91726 36 28.1 4.83 Heat shock protein cognate 71 HSC71 [Rivulus marmoratus] gi|7960186 730 71833 36 18.6 5.28 Hedgehog acyltransferase like [Gallus gallus] gi|118085466 62 57933 4 6.8 6.89 Hemoglobin subunit beta/beta~ (Hemoglobin beta/beta~ chain) (Beta/beta~-globin)gi|122618 266 16364 11 26.7 8.98 Hemoglobin-A alpha gi|211114 415 15492 18 35.2 9.1 Hexokinase 1 [Gallus gallus] gi|45383904 82 103847 4 5.8 6.32 High density lipoprotein binding protein [Homo sapiens] gi|4885409 46 141979 1 1.2 6.43 Histone cluster 1, H2bn [Bos taurus] gi|126165296 108 13915 3 11.9 10.31 Histone H1.03 gi|121896 130 22513 6 11.6 10.96 Histone H2A.2 [Homo sapiens] gi|31979 203 13898 5 19.8 10.21 HIV-1 Nef interacting protein [Homo sapiens] gi|1800303 89 45604 3 9.2 6.92 Homeo box D10a [Danio rerio] gi|18858857 42 39432 3 6.1 9.06 Human P5 isoform 2 [Gallus gallus] gi|50745031 80 49157 7 17.2 5.02 Human type 1 inositol 1,4,5-trisphosphate receptor [Gallus gallus] gi|118097075 65 310186 2 1.2 5.93 Hypoxia up-regulated 1 [Gallus gallus] gi|57528712 93 112534 4 6.8 5.14 Inhibitor of apoptosis protein 1 gi|1184316 85 69568 3 1.5 5.71 Integrator complex subunit 3 (Int3) gi|75042457 38 119564 2 3.7 5.54 Integrin, beta 1 (fibronectin receptor, beta polypeptide, [Gallus gallus] gi|86129418 57 91802 2 2.2 5.23 Inward rectifier potassuim channel 10 [Rattus norvegicus] gi|609668 44 42766 1 3.4 8.84 Ionotropic Glutamate Receptor-Like Glurdelta2 In The Apo Form gi|157836482 47 29864 2 5.3 5.15 Katanin p60 (ATPase-containing) subunit A 1 [Gallus gallus] gi|113206090 38 56289 2 1.2 7.04 Killer cell immunoglobulin-like receptor[Ornithorhynchus anatinus] gi|149412118 85 68041 7 10.4 4.5 -like protein KIF1A (Axonal transporter of synaptic vesicles) gi|2506794 48 193144 2 1.5 5.85 Lactate dehydrogenase B [Gallus gallus] gi|45383766 723 36694 34 35.4 7.07 Laminin-binding protein [Homo sapiens] gi|34234 49 31888 2 5.3 4.84 lectin, mannose-binding, 1 [Gallus gallus] gi|71897199 51 56712 3 7 5.57 Leucine-zipper-like transcriptional regulator 1 (LZTR-1) isoform 1 [Bos taurus] gi|119909660 43 95507 3 2.5 6.1 LLRep3 protein gi|200812 46 24462 2 10.9 9.81 Low density lipoprotein-related protein 1 [Gallus gallus] gi|45382557 364 525788 20 3 5.05 Low density lipoprotein-related protein 2 [Monodelphis domestica] gi|126326524 374 526770 16 2.6 4.86 Lysosomal membrane glycoprotein A gi|212254 279 45205 9 11.8 6.79 Lysosome-associated membrane glycoprotein LAMP-2a gi|551493 96 27424 3 4.8 6.57 Malate dehydrogenase 1, NAD (soluble) [Gallus gallus] gi|57530355 308 36748 20 31.1 6.92 Malate dehydrogenase 2, NAD (mitochondrial) [Gallus gallus] gi|50758110 605 37401 27 42.5 8.83 Mannose 6-Phosphate Receptor [Gallus gallus] gi|1183911 40 14692 2 16.2 4.32 Matricin gi|347839 53 61021 2 3.9 6.23 Mitochondrial Aspartate Aminotransferase gi|443542 275 45188 12 28.2 9.13 Mitochondrial ATP synthase gamma-subunit [Danio rerio] gi|41152375 54 32285 2 7.5 9.43 Mitogen-activated protein kinase kinase kinase kinase 4 [Gallus gallus] gi|71895623 67 140676 3 0.6 8.89 Mixed-lineage leukemia-like protein [Patagonotothen tessellata] gi|99078956 46 19922 2 3.2 10.83 mLGP85/LIMP II [Gallus gallus] gi|50746651 136 54272 5 9.8 5.38 MOB1 [Homo sapiens] gi|38194905 60 10552 4 12.1 9.34 Moesin (Membrane-organizing extension spike protein) [Monodelphis domestica] gi|126342091 40 71144 2 3.8 5.98 Multidrug resistance protein gi|307375 81 21710 4 14.3 5.84 Mutant cysteine-rich FGF receptor [Gallus gallus] gi|1480467 218 126226 11 11.3 6.53 basic protein [Gallus gallus] gi|45384134 115 18797 7 32.2 11.6 Myelin P0 protein precursor () (Myelin peripheral protein) (MPP)gi|585535 110 27621 9 19.3 9.59 Myoferlin isoform 1 [Gallus gallus] gi|118092845 58 235819 2 1.5 5.59 Myomegalin [Danio rerio] gi|41054021 48 137912 2 0.8 5.05 Myosin heavy chain-B non muscle gi|625058 98 32386 6 19.5 7.92 Myosin VI [Gallus gallus] gi|45382045 190 148993 7 7.2 8.81 Myosin, heavy polypeptide 9, non-muscle [Gallus gallus] gi|45382693 492 227446 31 12.7 5.47 Myotonic dystrophy kinase [Homo sapiens] gi|181603 38 69483 2 3 4.92 N-ethylmaleimide sensitive fusion protein [Cricetulus longicaudatus] gi|49518 121 83811 5 5.6 6.38 Na-K-2Cl 1 [Xenopus laevis] gi|147904042 340 127345 28 7.6 6.13 Na+-dependent glutamate/aspartate transporter [Gallus gallus] gi|8132399 58 24510 1 8.8 5.33 Na+/K+ transporting ATPase, alpha 1 polypeptide [Gallus gallus] gi|45382945 14120 113528 626 48 5.5 Na+/K+ transporting ATPase, beta 4 polypeptide [Gallus gallus] gi|113206084 899 36852 58 24.9 7.98 Natural killer cell enhancing factor isoform 4 [Gallus gallus] gi|50751518 769 22529 32 45.7 8.24 NCAM1, Neural cell adhesion molecule [Homo sapiens] gi|2190958 44 137652 2 1 5.54 Nesprin-3 [Gallus gallus] gi|118092141 47 110265 3 0.7 5.88 Nicastrin [Gallus gallus] gi|38607472 62 80214 2 5.4 5.8 Niemann-Pick C1 [Gallus gallus] gi|118086893 51 142999 4 3.1 5.52 NmrA-like family domain containing 1 [Gallus gallus] gi|71897147 222 32726 7 14.2 7.77 NODAL modulator 2 [Gallus gallus] gi|118098010 39 133977 2 2.4 5.42 Novel protein vertebrate vasodilator-stimulated phosphoprotein (VASP) [Danio rerio]gi|122890995 51 46932 2 7.4 8.74 Nucleobindin 2 [Gallus gallus] gi|57530004 111 53847 5 7.9 5.02 Nucleoside diphosphate kinase (NDK) (NDP kinase) gi|127987 74 17433 3 20.5 8.63 Olfactory receptor Olr390 [Gallus gallus] gi|118081860 48 36150 2 3.1 8.8 Otoferlin [Gallus gallus] gi|118089149 1048 229785 50 20.2 5.62 Outer mitochondrial membrane cytochrome b5 [Gallus gallus] gi|71895491 174 16204 5 23.6 5 p78-related protein gi|190138 40 78985 1 4.2 8 Parkinson disease (autosomal recessive, early onset) 7 [Gallus gallus] gi|45383015 66 20159 2 8.5 6.32 Peptidyl arginine deiminase, type III [Gallus gallus] gi|45384274 61 75303 3 6.7 5.76 Peptidylprolyl isomerase B (cyclophilin B) [Gallus gallus] gi|45382027 263 22456 10 19.3 9.4 Peroxiredoxin 1 [Rattus norvegicus] gi|109465923 75 11175 4 18 5.76 Pgrmc2 protein [Xenopus tropicalis] gi|39794459 54 25054 3 6.3 4.85 Phosphatidylethanolamine-binding protein 1 (PEBP-1) [Gallus gallus] gi|50756703 225 21115 7 35.8 6.96 Phosphofructokinase [Gallus gallus] gi|23821298 71 84939 2 5.2 6.75 Phosphoglycerate kinase 1 [Gallus gallus] gi|45384486 153 45087 9 16.8 8.31 Phosphoglycerate mutase 1 (brain) [Gallus gallus] gi|71895985 383 29051 25 48.8 7.03 Phosphopyruvate-hydratase alpha-enolase; carbonate dehydratase [Homo sapiens]gi|693933 238 47421 15 30.6 7.01 Phosphorylase, glycogen; brain [Gallus gallus] gi|71895729 52 97296 3 4.6 5.97 Piccolo [Mus musculus] gi|27372317 36 564472 1 0.4 6.13 PIH1 domain containing 2 [Bos taurus] gi|84000353 43 36364 2 2.9 5.16 PKM2 protein [Bos taurus] gi|73587283 1514 62016 67 26 8.62 4, [Danio rerio] gi|125818420 44 121598 2 2.3 9.11 Plasma membrane calcium ATPase isoform 2 (PMCA2) gi|179734 100 133824 2 3.2 5.7 Pleckstrin and Sec7 domain containing 2 [Homo sapiens] gi|14150035 63 85292 1 1.6 5.04 Plexin 2 gi|118082199 96 213037 7 3.9 5.68 Poly(A) binding protein, nuclear 1 [Homo sapiens] gi|4758876 38 32843 2 3.3 5.04 Polymerase (RNA) III (DNA directed) polypeptide H [Gallus gallus] gi|118082710 42 23459 3 5.8 4.41 Postreplication repair protein hRAD18p [Monodelphis domestica] gi|126336381 38 87191 3 0.8 9.21 Potassium channel tetramerisation domain containing 14 [Rattus norvegicus] gi|34857847 42 30713 1 12.4 7.63 Potassium voltage-gated channel, subfamily Q, member 1 [Gallus gallus] gi|118091304 88 72899 3 2.2 9.67 Ppar Gamma gi|5107774 54 30833 2 3.7 5.76 Pro-enkephalin gi|1093055 58 18589 2 11.8 5.14 Progesterone receptor membrane component 2 [Gallus gallus] gi|57530130 158 21685 4 15.9 5.26 Proliferation associated (pag) [Ornithorhynchus anatinus] gi|149632365 222 22406 11 25.6 6.96 Prolyl-4-hydroxylase (AA 5 - 494) [Gallus gallus] gi|63739 347 55174 23 30.6 4.66 Protein disulfide isomerase family A, member 4 [Gallus gallus] gi|57530768 381 71285 34 32.7 4.96 Protein disulfide isomerase-associated 3 precursor [Gallus gallus] gi|45383890 716 56546 43 51.9 5.76 Protein Kinase A Variant gi|50513587 42 40568 2 3.1 8.54 Protein PP4-X gi|189617 462 36262 19 10.6 5.65 Protocadherin 2A16 [Takifugu rubripes] gi|119514193 49 103866 2 1.7 5.15 Pyruvate kinase, muscle [Gallus gallus] gi|45382651 1985 58434 118 70.8 7.29 Rab GDI [Homo sapiens] gi|285975 143 51088 5 4.3 5.94 Rab GDI alpha [Rattus norvegicus] gi|396431 116 51058 3 11.2 5.05 Rab-10 (ORA1) gi|131847 172 22837 11 17 8.26 Rab-11B (ORA3) gi|131849 118 24654 5 16.1 5.64 Rab-33 gi|3023913 72 24944 3 7.8 6.84 Rab-5B gi|75571188 70 23828 3 18.6 8.29 RAB14, member RAS oncogene family [Rattus norvegicus] gi|16758368 297 24140 16 48.8 5.85 Rab15 protein [Mus musculus] gi|15489394 77 19558 4 13.1 5.93 RAB18, member RAS oncogene family [Mus musculus] gi|6755258 51 23306 2 7.3 5.24 RAB1A, member RAS oncogene family [Homo sapiens] gi|4758988 688 22891 28 37.1 5.93 Rab2 gene gi|1588651 176 24617 11 28.2 6.22 RAB21, member RAS oncogene family [Xenopus tropicalis] gi|62858707 86 24495 2 7.7 8.1 Rab3 GTPase-activating protein catalytic subunit, (Rab3-GAP p130) (Rab3-GAP) gi|62510941 41 87558 1 1.3 5.56 RAB33B, member of RAS oncogene family [Mus musculus] gi|8394133 72 26206 3 7.4 7.62 RAB35, member RAS oncogene family [Homo sapiens] gi|5803135 78 23296 5 13.9 8.52 RAB3C, member RAS oncogene family isoform 2 [Mus musculus] gi|149264762 45 25362 2 5.9 4.98 RAB4B protein [Homo sapiens] gi|45708726 94 13642 5 19.8 9.26 RAB5A, member RAS oncogene family isoform 1 [Macaca mulatta] gi|109131470 52 23854 2 6.5 8.9 Rab5c-like protein, Canis familiaris Rab5c protein, gi|508285 45 23781 2 13 8.87 RAB6A, member RAS oncogene family [Mus musculus] gi|13195674 71 23689 3 10.6 5.42 Rab7 [Mus musculus] gi|1050551 345 23829 15 30 7.53 Rabphilin 3A homolog [Xenopus laevis] gi|147900229 37 78519 1 1.2 8.18 RAP-1B homologue [Ciona intestinalis] gi|74096327 36 21326 2 14.1 5.99 Rap1b gi|595280 93 21201 4 14.1 5.37 Ras GAP IQGAP1 [Gallus gallus] gi|118096063 234 229796 10 4.7 8.66 Ras P21 gi|131873 135 21643 4 28 5.16 Ras-related protein O-Krev precursor gi|131854 67 21260 2 14.1 5.69 Related RAS viral (r-ras) oncogene homolog 2 [Gallus gallus] gi|57530014 71 23508 1 5.9 5.74 Reticulocalbin 2 [Gallus gallus] gi|118095590 67 35689 2 9.9 4.43 Reticulon 3w [Gallus gallus] gi|38605959 143 22091 5 6.4 6.36 RGS9-1 anchoring protein R9AP [Monodelphis domestica] gi|126296012 48 26414 1 3.4 5.55 Rho GDP dissociation inhibitor (GDI) alpha [Danio rerio] gi|39645438 65 23147 3 8.4 5 Ribophorin 1 gi|118096917 90 67433 4 9.1 6.46 Ribophorin II [Gallus gallus] gi|57529367 111 69085 2 7.3 5.82 Ribosomal protein 60S L5-A gi|132983 99 34312 3 4.7 9.66 Ribosomal protein L18 [Gallus gallus] gi|44968046 146 18895 5 18.1 11.84 Ribosomal protein L21 isoform 2 [Gallus gallus] gi|50731019 54 18622 2 10 10.49 Ribosomal protein L7 [Gallus gallus] gi|57530626 58 28819 5 26.8 10.83 Ribosomal protein P0 [Gallus gallus] gi|45384494 213 34435 6 23.7 5.72 Ribosomal protein S27a [Mus musculus] gi|94400086 45 15111 3 9.8 9.43 Ribosomal protein S3 [Gallus gallus] gi|71895095 89 27019 9 31.6 9.68 Ribosomal protein S6 [Gallus gallus] gi|6601470 44 28577 2 7.3 10.83 Saccharopine dehydrogenase (putative) [Gallus gallus] gi|61097999 703 47224 25 39.4 9.13 SEC22 vesicle trafficking protein-like 1 [Mus musculus] gi|6755448 156 24896 5 25.1 8.67 Secretory carrier SCAMP1 [Gallus gallus] gi|118095546 84 36433 2 4 8.79 SET domain containing 5 [Ornithorhynchus anatinus] gi|149634114 48 159670 2 0.7 9.41 Sh2d5 protein [Gallus gallus] gi|118101267 49 35928 1 2.8 9.3 Small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2) gi|2833357 41 5796 3 26 6.18 SNAP gamma [Ornithorhynchus anatinus] gi|149411293 43 34861 2 2.6 5.44 Solute carrier family 1, member 3, EAAT1, GLAST-1 gi|232176 127 59830 2 6.4 8.51 Solute carrier family 12 member 2 (Basolateral Na-K-Cl symporter) gi|1709293 425 131666 30 9 6.8 Solute carrier family 8 member 3 [Acris crepitans] gi|123965123 38 43066 2 4 5.41 Sorcin [Gallus gallus] gi|124249424 182 22208 7 27.3 5.37 Spectrin alpha nonerythroid gi|179106 48 284905 1 0.4 5.22 Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) [Gallus gallus] gi|110227609 825 285986 48 20.1 5.21 Spectrin, beta, non-erythrocytic 1 [Gallus gallus] gi|118087525 1387 274739 70 23 5.37 Spir-2 protein [Mus musculus] gi|27151755 71 81470 3 1.3 7.19 Statin-related protein gi|206440 168 50649 11 16.2 9.05 Surfeit 4 [Gallus gallus] gi|45383444 90 30827 3 11.5 7.64 Synaptobrevin SYBII, VAMP2 gi|606978 50 9445 2 29.3 6.07 Synaptojanin 2 isoform beta [Mus musculus] gi|3241985 46 128876 6 0.8 6.78 Synaptotagmin VIIgamma [Equus caballus] gi|149725300 41 84184 1 1.3 9.63 Syntaphilin gi|21362912 38 58752 1 5.8 5.65 Syntaxin 12 [Gallus gallus] gi|118101546 85 30950 5 16.2 5.14 Syntaxin 7 [Gallus gallus] gi|61098428 80 29438 1 5.4 5.29 Syntaxin 8 [Gallus gallus] gi|71897371 41 26928 1 7.6 5.56 Syntaxin binding protein 3, Munc 18-3 [Gallus gallus] gi|119331098 44 60088 1 1.5 6.56 syntrophin beta 1 [Gallus gallus] gi|57530105 50 57180 1 3.3 8.47 Synuclein SYN2 [Rattus sp.] gi|241081 48 15859 1 6 9.76 T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha) gi|13959582 123 60974 2 4.1 5.69 TBP-associated factor 11 [Homo sapiens] gi|5032151 58 23350 2 4.7 4.78 Tectorin alpha [Gallus gallus] gi|45385817 58 241795 4 1.3 5.35 2 (testicular) [Ornithorhynchus anatinus] gi|149638496 43 50016 5 3.7 5.76 Testis expressed protein 14 [Gallus gallus] gi|118100294 46 119332 2 1.4 5.55 Thioredoxin domain containing 4 (endoplasmic reticulum) [Gallus gallus] gi|50736203 68 47289 2 6.4 5.37 Thioredoxin peroxidase [Homo sapiens] gi|5453549 79 30749 3 8.9 5.86 THY1 [Gallus gallus] gi|30316401 78 18391 2 7.5 7.6 Toll interacting protein [Gallus gallus] gi|57529999 60 30748 2 5.1 5.03 Trans-Golgi p230 [Gallus gallus] gi|118086218 45 257761 2 0.4 5.21 Transient receptor potential cation channel, subfamily M, member 1 [Canis familiaris]gi|73951155 45 202815 1 1.1 6.9 Transient receptor potential cation channel, subfamily V, member 3 [Mus musculus]gi|21492638 41 91374 1 1.6 5.9 Transmembrane emp24 domain-containing protein 10 [Gallus gallus] gi|57529934 336 25016 11 21.9 6.37 Transmembrane protein 33 [Homo sapiens] gi|8922491 97 28275 2 4.9 9.75 TRIM5/cyclophilin A fusion protein [Aotus trivirgatus] gi|50301248 41 54865 2 5.7 6.72 Triose Phosphate Isomerase gi|230359 325 26755 23 49 7.26 gi|438880 51 28760 3 9.7 4.69 C-like protein gi|223036 104 16696 3 10.8 4.12 Tubulin alpha chain (Alpha T6) gi|549052 293 50820 17 27.3 4.94 Tubulin beta chain (Beta-tubulin) gi|135490 238 50285 12 28.5 4.78 Tubulin, beta 5 [Mus musculus] gi|7106439 1030 50095 40 39 4.78 Tubulin, beta 6 [Mus musculus] gi|27754056 174 50514 8 14.1 4.8 Tubulin, delta 1 (predicted), isoform CRA_b [Rattus norvegicus] gi|149053750 46 51375 2 8.4 6.79 Tumor-associated calcium signal transducer 1 [Gallus gallus] gi|60302776 277 35136 9 19 7.42 U-snRNP-associated cyclophilin [Ornithorhynchus anatinus] gi|149411062 38 62094 3 8.4 8.3 Ubiquitin gi|229532 230 8446 20 67.6 6.56 Ubiquitin carboxyl-terminal esterase L1 [Taeniopygia guttata] gi|115391986 41 25500 2 12.9 5.83 UDP glycosyltransferase 8 (UDP-galactose ceramide galactosyltransferase) [Gallusgi|45383714 gallus] 41 61730 2 4.6 9.42 Unconventional SNARE in the ER 1 homolog isoform 2 [Mus musculus] gi|21630273 43 16349 4 4.8 9.41 Vacuolar ATP synthase subunit B (Vacuolar proton pump subunit B) gi|1718088 57 50536 2 5.7 5.31 Vacuolar H+ ATPase E1 [Gallus gallus] gi|57525423 70 26159 3 6.2 7.74 Vacuolar H+-ATPase A subunit gi|162705 40 68803 1 1.9 5.41 Vacuolar protein sorting 35 [Gallus gallus] gi|57524880 112 92504 2 1.8 5.38 Valosin-containing protein [Xenopus tropicalis] gi|54020867 205 89864 8 11.6 5.17 VAMP (vesicle-associated membrane protein)-associated protein B and C [Gallus gallus]gi|57529406 129 27427 5 11.5 6.92 Vamp-associated protein 33kDa; VAP-33 gi|4191319 172 27528 6 11.6 8.8 Variable lymphocyte receptor A cassette [Petromyzon marinus] gi|140134983 42 5103 2 18.6 9.69 Very large inducible GTPase 1 [Danio rerio] gi|125856017 61 187490 2 0.9 6.08 Vesicle amine transport protein 1 homolog (T californica) [Gallus gallus] gi|118103033 43 41993 1 4.2 6.18 Vesicle-associated membrane protein 3 [Gallus gallus] gi|87196326 234 11737 6 38.5 9.25 Vesicle-associated membrane protein 7 [Gallus gallus] gi|71895505 114 25008 2 7.3 8.48 Villin 1 [Gallus gallus] gi|118085502 81 97854 3 5.3 5.77 Voltage-dependent anion-selective channel protein 2 (VDAC-2) gi|11134020 614 30162 23 40.1 8.63 Voltage-dependent calcium channel subunit alpha 1A [Bos taurus] gi|10178648 44 12761 1 13.6 6.96 Vomeronasal receptor V1RF3 isoform 1 [Equus caballus] gi|149738010 700 285441 37 14.4 5.22 WAP four-disulfide core domain 12 precursor [Homo sapiens] gi|20069858 41 12612 2 12.6 5.35 Zeta polypeptide 14-3-3, [Gallus gallus] gi|71897035 399 27929 20 45.7 4.73 Zinc finger protein 157 (HZF22) [Canis familiaris] gi|74007352 38 59795 3 1.6 9.03 Zinc finger protein 2 [Equus caballus] gi|149727338 37 49878 2 2.1 8.44 Zinc finger protein Ci-ArfGAP-11 [Ciona intestinalis] gi|114145433 41 110693 2 1.4 6.27 Supplemental Table 3

Protein description Accession number Protein score Protein mass Protein matches Protein coverage Isoelectric point

Actin beta (beta~-actin) [Homo sapiens] gi|28336 787 42128 42 34.4 5.22 Actin, muscle gi|113283 256 42325 10 13.2 5.29 Adaptin alpha A homolog [AA 159-977] [Homo sapiens] gi|4314340 109 90845 4 4.4 5.89 ADP-ribosylation-like factor 6 interacting protein 5 [Bos taurus] gi|62460474 56 21651 2 10.1 9.48 ADP-ribosyltransferase (NAD+) poly (ADP-ribose) polymerase) [Bos taurus] gi|27807449 104 114270 3 4 8.98 ADP/ATP translocase 2 (Adenine nucleotide translocator 2) gi|113459 626 33102 28 24.2 9.76 Aldehyde dehydrogenase 3A2 [Bos taurus] gi|156120617 73 54497 2 6.6 7.56 Aldolase A [Bos taurus] gi|156120479 293 39925 11 19.5 8.45 Alpha enolase [Trachemys scripta] gi|4416385 1241 40532 36 26.5 5.35 Alpha- [Rattus norvegicus] gi|55622 74 55712 2 2.6 5.2 Alpha-tubulin [Homo sapiens] gi|37492 3762 50810 133 55.7 5.02 Annexin 4 gi|4033507 87 36034 2 9.7 5.71 Annexin 5, CaBP37 isoform [cattle, brain, Peptide, 320 aa] gi|260138 226 35992 7 27.2 4.86 Annexin 6 [Bos taurus] gi|157151716 712 76202 28 25.3 5.64 AP-1 complex subunit beta-1 (Beta1-adaptin) gi|1703167 89 105452 3 4.4 4.94 AP-2, adaptor-related protein complex 2, beta 1 subunit isoform b [Homo sapiens] gi|4557469 238 105398 6 3.8 5.22 AP180, assembly protein 180 [Rattus norvegicus] gi|55725 50 91601 1 1.3 4.75 Apolipoprotein O [Bos taurus] gi|115497246 75 22662 3 13.1 9.24 Apoptosis-inducing factor AIF isoform 2 [Bos taurus] gi|76658657 68 67115 2 5.1 9.24 Aspartate aminotransferase 1 [Bos taurus] gi|29135295 66 46669 3 11.4 7.09 Aspartate beta-hydroxylase [Bos taurus] gi|27807467 203 85402 4 7.6 5.05 Band 4.1-like protein 2 isoform 2 [Canis familiaris] gi|73945902 115 109695 2 3.6 5.23 Basigin [Bos taurus] gi|115496127 464 29982 17 32.8 5.65 Bassoon protein [Homo sapiens] gi|3928704 38 412064 1 0.5 7.35 BBC1 [Homo sapiens] gi|29383 87 24334 3 10 11.65 Brain abundant, membrane attached signal protein 1 [Bos taurus] gi|27807507 140 22997 7 33.5 4.55 Brain-associated small cell lung cancer antigen - human (fragment) gi|627391 118 1908 2 100 4.14 C-type natriuretic peptide precursor gi|728854 50 15224 3 5.2 5.39 Calcium ATPase (hPMCA4) isoform 5 [Bos taurus] gi|119908026 106 134848 4 4.1 6.07 Calcium/calmodulin-dependent protein kinase II delta2 isoform [Homo sapiens] gi|4426595 90 56889 2 6.4 7.01 Calnexin [Bos taurus] gi|157785567 338 68189 15 9.9 4.48 Carbonic anhydrase 14 isoform 1 [Bos taurus] gi|61809435 114 38082 3 9.8 6.57 Caveolin [Homo sapiens] gi|38516 56 20640 2 4.5 5.95 Cell cycle exit and neuronal differentiation 1 [Bos taurus] gi|122692303 385 14323 10 45.9 9.59 Cis-11-retinol dehydrogenase gi|1054531 117 34777 2 5 9.06 Clathrin heavy chain 1 [Homo sapiens] gi|4758012 615 193260 25 17.9 5.48 Coactivator 100 kDa gi|799177 68 100313 1 1.5 6.62 Cofilin 1 (non-muscle) [Homo sapiens] gi|5031635 158 18719 4 27.1 8.22 Coiled-coil-helix-coiled-coil-helix domain containing 3 [Bos taurus] gi|78365273 60 26312 2 11.5 8.52 Creatine kinase, mitochondrial 1, ubiquitous [Mus musculus] gi|6753428 259 47373 14 24.6 8.39 Cysteine string protein [Bos taurus] gi|1232165 70 19601 2 24 5.39 Cytoplasmic dynein intermediate chain 2B gi|1151093 62 70748 2 5.5 5.11 DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 [Bos taurus] gi|115495959 116 83331 4 4.2 6.81 Dynamin gi|181849 106 97745 5 4.3 6.93 Dynein, cytoplasmic, heavy polypeptide 1 isoform 3 [Bos taurus] gi|119914141 316 548197 9 2.5 6.03 Elongin A2 [Macaca mulatta] gi|109122103 43 84662 4 0.8 9.58 Enolase 1 [Bos taurus] gi|87196501 1565 47639 57 49.3 6.37 Enolase gamma gi|182118 567 44568 12 8.3 4.94 Epoxide 1, microsomal (xenobiotic) [Bos taurus] gi|77736205 115 52449 2 5.3 7.23 Gamma-aminobutyric acid transporter type 3, GAT-3 [Bos taurus] gi|119914859 175 57589 4 6.6 5.6 Gelsolin, cytosolic - mouse gi|90508 62 81113 1 2.5 5.53 Glial fibrillary acidic protein [Bos taurus] gi|1561571 172 49479 10 21.3 5.3 Glutamate dehydrogenase 1 [Homo sapiens] gi|4885281 94 61701 3 7.7 7.66 Glutamate--ammonia [Homo sapiens] gi|31831 63 42748 2 7.5 6.61 Glutamic-oxaloacetic transaminase 2, (aspartate aminotransferase 2) [Bos taurus] gi|27807377 237 47882 7 14.2 9.19 Glutamine synthetase [Bos taurus] gi|95006991 804 42632 34 19.6 6.38 Glutathione S-transferase M3 [Bos taurus] gi|114053087 203 27174 8 19.6 6.83 Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) (EC 1.2.1.12) - pig gi|65987 3855 35914 133 35.2 6.9 Growth regulated nuclear 68 protein gi|226021 74 67394 2 2 8.95 GTP-binding protein gi|162760 197 25067 8 17.7 4.86 Guanine nucleotide binding protein, alpha transducing 1 [Mus musculus] gi|6680041 749 40397 30 44 5.4 Guanine nucleotide-binding protein, beta-1 subunit [Mus musculus] gi|6680045 147 38151 9 12.6 5.6 H+ transporting ATP synthase, alpha subunit [Bos taurus] gi|27807237 2146 59797 72 45.9 9.21 H+ transporting ATPase, lysosomal 70kD, V1 subunit A, isoform 1 [Macaca mulatta]gi|109033102 521 68687 25 24 5.35 Heat shock protein 70 cognate gi|309319 850 71021 49 39.8 5.37 Heat shock protein beta-1, (HSP 27) gi|85542053 590 22436 18 41.3 5.98 Hexokinase 1 [Bos taurus] gi|60592784 431 103338 20 20.6 6.29 Histone H1.1 gi|121903 433 10359 20 32.7 10.49 Homeobox prox 1 [Homo sapiens] gi|7706322 87 28165 3 13.9 6.19 Inosine monophosphate dehydrogenase 1 [Bos taurus] gi|118150800 525 61634 20 33.3 6.3 Internexin neuronal protein, alpha [Bos taurus] gi|115494964 263 55533 14 26.5 5.34 Kinectin 1 [Bos taurus] gi|156121057 103 150936 4 3.5 5.64 Lactate dehydrogenase B [Bos taurus] gi|27806561 203 36886 9 21 6.02 Laminin-binding protein [Homo sapiens] gi|34234 72 31888 2 4.6 4.84 Malate dehydrogenase, mitochondrial precursor gi|118572778 411 36102 17 27.5 8.82 Membrane anchor R9AP [Bos taurus] gi|21622626 113 24866 4 17.3 6.24 Membrane receptor p63 [Bos taurus] gi|564 62 61616 2 2.1 6 Membrane steroid binding protein [Bos taurus] gi|7689365 115 20860 4 17.8 4.61 -associated protein 1B isoform 2 [Bos taurus] gi|76646182 235 270857 7 3.3 4.72 Microtubule-associated protein 4 isoform 1 [Bos taurus] gi|22138804 103 71363 5 8.8 9.4 Mitochondrial glutamate carrier 1 [Bos taurus] gi|115495639 81 34965 4 7.8 9.42 Mitofilin [Bos taurus] gi|114051089 158 83306 5 7.5 6.44 Mitosis-specific chromosome segregation protein SMC1 homolog [Homo sapiens] gi|999380 83 143743 3 2.2 7.51 Munc 18-1 [Bos taurus] gi|27807117 567 67911 28 30 6.49 MYO15 unconventional myosin [Mus musculus] gi|3168866 43 202151 3 0.3 9.01 Myosin heavy chain nonmuscle gi|212449 58 229866 2 1.7 5.42 Myosin VI [Bos taurus] gi|119901099 593 149935 21 13.6 8.76 Myosin-VIIa [Gallus gallus] gi|118103678 58 105691 2 1 8.72 Myosin, heavy chain 14 isoform 4 [Bos taurus] gi|119910817 96 232112 6 3.7 5.55 Myristoylated alanine-rich C-kinase substrate (MARCKS) (ACAMP-81) gi|148872484 123 31817 4 19.8 4.41 N-ethylmaleimide-sensitive factor [Bos taurus] gi|119912502 627 86140 26 18.7 7.86 N-myc downstream-regulated gene 2 isoform b isoform 2 [Canis familiaris] gi|73977279 84 31291 3 10.2 5.35 Na(+)/K(+)/Ca(2+)-exchange protein 1 gi|17865507 69 131874 3 2.7 4.42 Na+, K+ transporting ATPase catalytic subunit gi|497763 2980 112987 98 27.5 5.22 Na+/K+ -ATPase alpha 3 subunit [Rattus norvegicus] gi|6978547 2392 113032 85 33.3 5.26 Na+/K+ -ATPase alpha 4 subunit [Macaca mulatta] gi|109017575 656 110398 25 8.2 6.03 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa [Bos taurus] gi|28603782 261 39524 4 10.5 6.52 NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa [Bos taurus] gi|27807355 252 80418 7 10.7 5.82 NADH dehydrogenase 24 kDa subunit (AA 6-217) [Bos taurus] gi|1364245 80 23771 3 15.6 5.71 Neural cell adhesion molecule 1, 140 kDa isoform precursor (N-CAM 140) (NCAM-140)gi|400398 274 94633 16 13.8 4.87 Neuroendocrine specific protein c homolog [Homo sapiens] gi|5107002 157 22557 4 7 9.17 protein (AA at 517) gi|387492 108 61357 9 8.7 4.66 Neurofilament triplet H protein (200 kDa neurofilament protein) [Bos taurus] gi|119909545 57 118361 2 2.7 8.44 Neurofilament triplet M protein (160 kDa neurofilament protein) (NF-M) [Bos taurus]gi|119921890 104 103608 6 4.7 4.94 Neuronatin, isoform CRA_c [Rattus norvegicus] gi|149043096 44 13692 1 7 11.38 Neuroplastin [Bos taurus] gi|115495671 92 31074 1 6.5 7.05 Neuropolypeptide h3 [human, brain, Peptide, 186 aa] gi|913159 92 21027 2 10.8 7.42 NIPSNAP1, non-neuronal SNAP25-like protein homolog 1 [Mus musculus] gi|6679066 62 33570 2 12 9.48 Nucleotidase 5 precursor [Bos taurus] gi|285642 48 63616 2 3.8 6.44 Numa1 protein [Rattus norvegicus] gi|71051118 50 71467 2 2.2 9.52 Oxoglutarate 2 carrier [Homo sapiens] gi|23844 272 34229 8 15.9 9.92 P63 protein [Bos taurus] gi|119892686 170 64605 6 9.8 5.71 Peptidyl-prolyl cis-trans isomerase B precursor (Cyclophilin B) gi|118090 67 22785 3 17.3 9.33 -2 (Retinal degeneration slow protein) gi|132211 490 39708 19 14.5 8.35 Peroxiredoxin 2 [Bos taurus] gi|27807469 213 22217 5 14.6 5.37 Phenylalanyl-tRNA synthetase, beta subunit [Bos taurus] gi|157279951 179 67039 9 15.6 7.15 Phosphatidylethanolamine-binding protein 1 (PEBP-1) gi|1352725 209 21087 3 16.6 6.96 Phosphofructokinase, muscle [Bos taurus] gi|115497288 1204 86095 47 27.5 8.56 Phosphoglycerate kinase gi|202423 170 44907 4 12 7.53 Phosphoglycerate mutase 1 (brain) [Homo sapiens] gi|4505753 73 28900 3 11.4 6.67 Plasma membrane calcium ATPase isoform 2 PMCA2 gi|179734 69 133824 2 2.3 5.7 Porin gi|190200 675 38639 24 25.4 6.32 Probable ATP-dependent RNA helicase DDX17 (DEAD box protein 17) gi|3122595 110 72953 3 3.7 8.82 Progesterone binding protein [Pan troglodytes] gi|114595991 251 26169 6 13.8 5.32 Prohibitin [Homo sapiens] gi|4505773 180 29843 10 24.3 5.57 Protein 14-3-3 zeta chain [cattle, brain, Peptide, 245 aa] gi|253706 169 27810 6 14.3 4.73 Proteolipid protein DM beta gi|544167 87 31887 2 5 5.12 Pyruvate kinase muscle 2 protein [Bos taurus] gi|73587283 994 62016 36 33.8 8.62 Rab GDI alpha [Rattus norvegicus] gi|396431 128 51058 2 8.5 5.05 Rab-10 (ORA1) gi|131847 146 22837 8 17 8.26 Rab-11B (ORA3) gi|131849 99 24654 4 11 5.64 Rab-8 (ORA2) gi|131848 81 24320 6 16.2 9.35 RAB14, member RAS oncogene family [Rattus norvegicus] gi|16758368 271 24140 10 39.1 5.85 RAB1A, member RAS oncogene family [Homo sapiens] gi|4758988 293 22891 19 32.7 5.93 RAB1B, member RAS oncogene family [Homo sapiens] gi|13569962 271 22328 17 26.4 5.55 RAB5A, member RAS oncogene family [Rattus norvegicus] gi|12083645 86 23828 3 11.6 8.32 RAB5B, member RAS oncogene family [Homo sapiens] gi|4506371 105 23920 3 18.1 8.29 Rab5c-like protein, Canis familiaris Rab5c protein gi|508285 87 23781 3 17.1 8.87 Rab7 [Mus musculus] gi|1050551 161 23829 5 11.6 7.53 Ras homolog gene family, member Q [Gallus gallus] gi|45383243 45 23987 1 9.3 5.95 Recoverin [Mus musculus] gi|6677693 50 23449 2 11.9 5.06 Reticulon 1 isoform A [Homo sapiens] gi|10863935 91 83851 2 1.7 4.62 Reticulon 3 isoform a [Homo sapiens] gi|5174655 209 25764 9 5.5 8.67 Reticulon 4 protein [Bos taurus] gi|157279064 240 70818 7 9.6 4.48 Retinal G protein coupled receptor [Bos taurus] gi|28461177 525 32340 21 14.4 8.48 Retinaldehyde-binding protein precursor gi|163653 372 36723 14 23.7 5 Retinol binding protein 3, interstitial [Bos taurus] gi|27806445 808 140181 31 20.8 5.14 Retinol dehydrogenase 12 (all-trans and 9-cis) [Bos taurus] gi|34365787 200 35605 6 17.1 9.67 Ribophorin I [Bos taurus] gi|129277520 251 68481 9 14.9 5.95 Ribosomal protein L11 [Homo sapiens] gi|495126 283 20331 9 7.9 9.6 Ribosomal protein L18 [Homo sapiens] gi|4506607 255 21735 9 19.7 11.73 Ribosomal protein S9 [Homo sapiens] gi|14141193 124 22635 6 21.6 10.66 Rom1 [Bos taurus] gi|1272503 61 37993 2 3.7 5.81 RPL9 protein isoform 1 [Bos taurus] gi|76607197 86 21761 3 15.7 9.72 S-adenosyl homocysteine hydrolase homolog [Homo sapiens] gi|2852125 56 56675 2 4.6 7.75 S- (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin)gi|114215 340 45418 16 28 6.08 S100 calcium binding protein A16 [Homo sapiens] gi|223029 121 10644 2 16.5 4.56 SEC22 vesicle trafficking protein-like 1 [Mus musculus] gi|6755448 295 24896 9 25.1 8.67 Sec61 beta subunit [Bos taurus] gi|115497008 48 9995 1 15.6 11.57 Septin-6 isoform 2 [Canis familiaris] gi|74008208 124 54004 4 7.4 6.56 Septin-7 (CDC10 protein homolog) gi|67472680 419 50544 13 21.2 8.86 SERPINE1 mRNA binding protein 1 [Homo sapiens] gi|12803339 299 44291 8 10.7 8.31 Sideroflexin 1 [Bos taurus] gi|62751841 131 35952 4 11.8 9.42 SNAP-25 protein - chicken gi|481203 232 28835 7 23.3 5.29 SNAP-alpha, (N-ethylmaleimide-sensitive factor attachment protein alpha) gi|3024627 107 33659 3 16.3 5.39 Solute carrier family 1, member 3, EAAT1, GLAST-1 [Bos taurus] gi|27807085 365 59724 11 10.7 8.23 Solute carrier family 16, member 1 [Bos taurus] gi|82617542 562 54718 16 12 8.24 Solute carrier family 2, facilitated member 1 (GLUT-1) gi|121753 162 50087 7 11.8 8.49 Solute carrier family 25 member 12, Calcium-binding protein Aralar1 gi|13124050 112 75108 6 7.1 8.58 Solute carrier family 25, member 4 [Gallus gallus] gi|57530120 555 33175 25 20.8 9.74 Solute carrier family 25, member A6 [Bos taurus] gi|32189336 625 33084 27 26.8 9.82 Solute carrier family 3, member 2 [Bos taurus] gi|59857795 374 63285 10 19.1 4.96 Spectrin alpha gi|179106 289 284905 10 4.4 5.22 Spectrin beta chain, brain 1, non-erythroid, (Fodrin) [Canis familiaris] gi|73969626 398 275123 14 8.1 5.38 Splicing factor proline/glutamine rich [Homo sapiens] gi|4826998 370 76216 14 18.5 9.45 Srp20 [Mus musculus] gi|2125864 71 14422 2 11.3 10.12 Statin-related protein gi|206440 403 50649 14 17.1 9.05 synaptic vesicle glycoprotein 2A gi|383109 62 83349 3 3.1 5.43 Synaptic vesicle glycoprotein 2B gi|207092 42 83393 1 1.3 5.37 Synaptobrevin SYBII gi|606978 130 9445 4 29.3 6.07 Synaptocanalin gi|383088 193 33469 6 18.4 5.13 Synaptogyrin gi|1587032 61 25953 2 5.1 4.49 Synaptophysin [Bos taurus] gi|27806797 115 33517 3 7.8 5.1 Synaptoporin [Rattus norvegicus] gi|13027428 57 29430 1 5.3 6.07 Synaptotagmin [Rattus rattus] gi|57643 141 47765 8 14 8.44 Syntaxin 3 [Bos taurus] gi|156120591 912 33190 25 26 5.25 Syntaxin 3B [Mus musculus] gi|924270 502 32658 13 18 5.26 T-complex polypeptide 1 [Homo sapiens] gi|36796 67 60869 2 4.1 6.03 Thy-1 cell surface antigen [Bos taurus] gi|77736475 136 18229 5 15.5 9.3 Transmembrane emp24 protein transport domain containing 4 [Mus musculus] gi|19527236 63 26233 2 8.8 8.33 Transmembrane protein 33 [Homo sapiens] gi|8922491 75 28275 1 4.9 9.75 Triosephosphate isomerase 1 [Bos taurus] gi|61888856 147 26901 6 16.1 6.45 -like protein gi|223036 40 16696 2 22.3 4.12 Tubulin beta chain (Beta-tubulin) gi|135490 4627 50285 181 66.7 4.78 Tubulin, beta 5 [Mus musculus] gi|7106439 4402 50095 171 63.7 4.78 Tubulin, beta 8 [Macaca mulatta] gi|109088011 275 50799 23 7.6 5.04 Tubulin, beta, 2 [Homo sapiens] gi|5174735 4589 50255 182 60.7 4.79 Tumor necrosis factor (TNF superfamily, member 2) [Danio rerio] gi|66773048 44 26919 1 4.1 5.96 ULIP2 protein [Mus musculus] gi|1915913 134 62531 6 17.1 5.95 Vacuolar isoform 2 of H+ATPase Mr 56,000 subunit [Homo sapiens] gi|37794 234 56823 9 17.4 5.57 Vacuolar proton ATPase [Homo sapiens] gi|313014 428 26271 14 16.8 8.45 Vacuolar proton pump subunit D (V-ATPase subunit D) - human gi|542837 84 32083 4 8.8 5.16 Valosin-containing protein isoform 3 [Canis familiaris] gi|73971210 92 89931 4 8.2 5.13 VAMP-associated protein B and C [Bos taurus] gi|129270105 133 27369 5 16.9 6.85 Vesicle-associated membrane protein-associated protein A [Bos taurus] gi|115496338 158 28067 5 17.7 8.8 gi|138535 199 53754 11 20.6 5.06 Voltage-dependent anion channel 1 [Mus musculus] gi|6755963 1367 30851 47 58.7 8.62 Voltage-dependent anion channel 3 [Mus musculus] gi|6755967 182 31076 7 19.1 8.96 Voltage-gated potassium channel gi|186798 61 96316 1 1.5 8.32 X-linked juvenile retinoschisis precursor protein [Bos taurus] gi|119920589 310 24746 11 26.5 5.64 Supplemental Table 4

Protein description Accession number Protein score Protein mass Protein matches Protein coverage Isoelectric point

Acetylcholinergic receptor M4 [Narudasia festiva] gi|156067640 45 16197 2 13.6 9.21 Aconitase 2, mitochondrial [Gallus gallus] gi|45383738 55 86535 4 5.9 8.05 Actin alpha 1 skeletal muscle protein [Homo sapiens] gi|169213772 57 51513 3 2.6 6.07 Actin beta [Gallus gallus] gi|63018 1678 42080 86 52.5 5.29 Actin cytoplasmic 2 [Boltenia villosa] gi|21703262 857 17662 37 35.2 4.86 Actin-gamma like protein [Mus musculus] gi|6425087 1518 44029 68 38.7 5.11 Actin, muscle-type (A2) gi|3121741 1051 42521 61 40.2 5.12 ADP/ATP translocase 2 (Adenine nucleotide translocator 2) (ANT 2) gi|113459 398 33102 17 17.4 9.76 repeat, SAM and basic leucine zipper domain-containing protein 1 gi|118572909 49 53638 3 3.4 5.31 Annexin 2 [Gallus gallus] gi|45382533 115 38901 12 39.8 6.92 Annexin 5 gi|62738641 116 36159 6 16.9 5.61 Annexin 6 [Gallus gallus] gi|50982399 165 75579 9 13.1 5.57 Annexin 8, VAC beta [Gallus gallus] gi|50749462 273 36938 13 26.9 5.24 BTB (POZ) domain containing 14A isoform 2 [Rattus norvegicus] gi|34853069 40 63811 2 1.9 5.73 C-type lectin superfamily 4, member G [Monodelphis domestica] gi|126323871 46 49680 3 1.8 8.65 Calmodulin gi|16974825 60 8483 3 39.5 3.9 Clathrin heavy chain 1 [Homo sapiens] gi|4758012 361 193260 24 13 5.48 Coagulation factor C homolog, cochlin (Limulus polyphemus) [Gallus gallus] gi|45384390 80 60016 6 7.7 8.61 Coatomer protein complex, subunit alpha [Gallus gallus] gi|71897175 78 140060 7 5.1 7.53 Coatomer subunit beta~ (Beta~-coat protein) (Beta~-COP) (p102) gi|544075 75 103153 3 4 5.15 Coiled-coil-helix-coiled-coil-helix domain containing 2 [Mus musculus] gi|18079334 50 15879 2 8.5 9.78 COL25A1 protein [Homo sapiens] gi|22477176 35 51490 2 7.9 9.77 Creatine kinase (EC 2.7.3.2) chain Bb - chicken gi|104630 217 44070 13 16.7 6.47 Cyclic 2~,3~-nucleotide 3~ phosphodiesterase [Gallus gallus] gi|45384252 80 47549 3 6.4 9.15 Cyclic AMP-regulated phosphoprotein, 21 kD [Ornithorhynchus anatinus] gi|149410059 39 26932 2 11.2 9.95 Cytochrome b5 fragment gi|229381 40 9567 3 37.3 5.2 Cytochrome P450 family 17 polypeptide 2 [Oreochromis niloticus] gi|148612548 41 58166 3 1.7 8.35 DEAH (Asp-Glu-Ala-His) box polypeptide 33 [Mus musculus] gi|56237887 43 76323 2 2.1 9 Dihydrolipoamide dehydrogenase [Gallus gallus] gi|71897021 428 54568 32 25.4 8.19 Dihydrolipoamide S-acetyltransferase [Gallus gallus] gi|118102025 875 72561 41 25.4 8.84 Dihydrolipoamide S-succinyltransferase [Gallus gallus] gi|61098338 166 49594 11 9.1 9.25 Dlg5 protein [Xenopus tropicalis] gi|110645390 52 36832 2 3.2 8.7 DnaJ (Hsp40) homolog, subfamily C, member 13 [Rattus norvegicus] gi|157817568 83 209303 5 2.8 6.57 DnaJ domain-containing protein RME-8 [Gallus gallus] gi|118085986 148 256634 14 6.6 6.35 Dullard homolog, like [Danio rerio] gi|55925373 48 28600 2 4.5 9.72 Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor Tu) (EF-Tu) gi|3122072 308 50467 24 22.9 9.1 Enolase A [Typhlonectes natans] gi|98979419 112 47637 6 14.3 6.53 Enolase alpha (2-phospho-D-glycerate hydro-lyase) (Tau-crystallin) gi|119338 112 47609 7 17.1 6.37 Enolase-1 beta [Chiloscyllium punctatum] gi|11999263 142 39672 7 16 5.88 Eukaryotic translation initiation factor 3 interacting protein [Gallus gallus] gi|60302722 79 66868 4 6.4 5.93 Ferritin, heavy polypeptide 1 [Gallus gallus] gi|45384172 42 21249 2 16.1 5.78 G protein, beta polypeptide 2-like 1 [Homo sapiens] gi|5174447 256 35511 12 24.3 7.6 Gelsolin [Gallus gallus] gi|45384386 267 86120 16 12.9 5.93 Globin beta [Homo sapiens] gi|4038415 75 6262 4 17.5 4.55 Globin-D [Gallus gallus] gi|63013 78 15770 2 11.3 7.01 Glucose-regulated protein precursor (GRP 78) gi|121570 71 72505 6 6.9 5.07 Glutathione S-transferase [Gallus gallus] gi|50729056 75 17330 3 17.4 9.67 Glyceraldehyde-3-phosphate dehydrogenase [Mus musculus] gi|6679937 4783 36072 154 33.9 8.44 H+ transporting ATP synthase [Gallus gallus] gi|45383566 42 60263 2 5.1 9.29 Heat shock 70 kDa protein (HSP70) gi|2495347 43 71218 6 3.1 5.73 Heat shock cognate 71 kDa protein [Canis familiaris] gi|74008507 114 44233 10 15.5 5.33 Heat shock protein 90kDa alpha (cytosolic) [Xenopus tropicalis] gi|118404692 53 82788 3 3.8 5.06 Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) gi|399861 256 16496 16 54.8 8.85 Heterogeneous nuclear ribonucleoprotein R isoform 2 [Homo sapiens] gi|5031755 70 71184 5 6 8.23 Histone H1.03 gi|121896 99 22513 6 10.7 10.96 Histone H2A.2 [Homo sapiens] gi|31979 189 13898 12 27 10.21 Histone H2B 7 (H2B VII) gi|110279003 101 13956 5 27 10.31 Histone H4, partial [Bos taurus] gi|119930610 243 11794 19 40.6 11.22 hnRNP U protein [Homo sapiens] gi|32358 136 89631 2 1.9 5.6 Homeo box D10a [Danio rerio] gi|18858857 38 39432 3 6.1 9.06 to rat ribosomal protein L23 gi|306549 101 16730 5 22.4 10.46 HUEL [Monodelphis domestica] gi|126331799 42 66500 2 2.2 8.72 Inner-ear [Rana catesbeiana] gi|6980088 54 56584 2 4.5 5.81 L21 ribosomal protein [Homo sapiens] gi|619788 56 17703 2 9.9 10.38 Laminin receptor precursor 67kD [Xenopus laevis] gi|148233658 90 34208 6 17.3 4.81 Laminin-binding protein [Homo sapiens] gi|34234 359 31888 17 29.1 4.84 Leucine rich repeat containing 16 [Bos taurus] gi|119915770 43 147732 2 1.1 7.55 Long chain fatty acyl CoA synthetase [Gobionotothen gibberifrons] gi|12746386 40 78470 2 1.7 6.32 Major vault protein [Gallus gallus] gi|57530557 203 94164 12 11.5 5.32 Malate dehydrogenase 2, NAD (mitochondrial) [Gallus gallus] gi|50758110 181 37401 11 19.7 8.83 Methyl-CpG-binding protein 2 [Monodelphis domestica] gi|126342171 36 74764 2 4.1 9.95 Mitochondrial ribosomal protein L7L12 [Homo sapiens] gi|1313962 43 21593 2 5.6 9.04 Mitochondrial trifunctional protein, alpha subunit [Gallus gallus] gi|45384238 58 83818 7 10.5 9.19 Moesin [Monodelphis domestica] gi|126342091 39 71144 2 3.8 5.98 Mvp protein [Danio rerio] gi|29179488 61 95054 3 1.3 5.48 [Gallus gallus] gi|45384134 124 18797 12 28.7 11.6 Myelin P0 protein precursor (Myelin protein zero) (MPP) gi|585535 429 27621 45 28.1 9.59 Myosin IIIA [Danio rerio] gi|45387587 49 203260 3 0.5 5.98 kinase (MLCK) [Gallus gallus] gi|118096343 39 104237 2 1.2 8.64 Myosin VI [Homo sapiens] gi|9280816 119 147324 8 3.2 8.75 Myosin, heavy polypeptide 9, non-muscle [Gallus gallus] gi|45382693 46 227446 3 2 5.47 Na(+)/K(+) ATPase alpha-1 subunit gi|2493013 1544 114012 52 10.2 5.32 Na+/K+ transporting ATPase, alpha 4 [Monodelphis domestica] gi|126307285 155 110198 7 4.9 5.4 Nascent polypeptide-associated complex alpha subunit [Homo sapiens] gi|5031931 67 23370 3 13 4.52 Novel protein [Danio rerio] gi|94732457 46 79050 3 1.1 6.5 Novel protein containing Rieske [2Fe-2S] domain [Xenopus tropicalis] gi|113931468 53 48263 2 2.6 5.35 Nuclear factor RIP140 [Monodelphis domestica] gi|126325183 49 106484 2 1.2 8.94 Oxoglutarate (alpha-ketoglutarate) dehydrogenase [Gallus gallus] gi|71897293 1118 116305 69 27 6.56 Oxysterol binding protein-like 6, [Danio rerio] gi|125825332 53 108522 2 1.5 7.59 Peptidylprolyl isomerase B (cyclophilin B) [Gallus gallus] gi|45382027 60 22456 8 25.6 9.4 Phospholipase C-like 4 [Rattus norvegicus] gi|109475915 40 162228 3 2.2 7.05 PKM2 protein [Bos taurus] gi|73587283 78 62016 9 10.8 8.62 Poly [ADP-ribose] polymerase 14 (PARP-14) [Danio rerio] gi|125826730 47 157372 3 0.6 8.4 Proliferation-associated protein 1, partial [Gallus gallus] gi|118129651 75 38840 8 20.1 8.64 Proto-oncogene protein [Hydrobates pelagicus] gi|112950272 56 19239 3 6 9.27 PTB-associated splicing factor [Gallus gallus] gi|118101662 48 69288 2 4.3 9.43 Pyruvate carboxylase gi|200246 41 103782 2 1.5 6.15 Pyruvate dehydrogenase (lipoamide) alpha 1 [Gallus gallus] gi|60302740 157 45041 5 6 8.19 Pyruvate dehydrogenase (lipoamide) beta [Gallus gallus] gi|50754481 117 39308 7 20.9 5.95 Pyruvate kinase, muscle [Gallus gallus] gi|45382651 104 58434 11 11.5 7.29 Rab-related GTP-binding protein [Homo sapiens] gi|1491714 40 25253 3 5.1 6.9 RAB14 protein [Mus musculus] gi|63087695 78 24123 5 25.1 5.63 Rab15 protein [Mus musculus] gi|15489394 40 19558 4 13.1 5.93 RAB1A, member RAS oncogene family [Homo sapiens] gi|4758988 176 22891 12 32.7 5.93 RAB33B, member of RAS oncogene family [Mus musculus] gi|8394133 40 26206 3 4.8 7.62 RAB35, member RAS oncogene family [Homo sapiens] gi|5803135 40 23296 4 10.9 8.52 RAB4B protein [Homo sapiens] gi|45708726 55 13642 5 19.8 9.26 Ral guanine nucleotide dissociation stimulator [Equus caballus] gi|149758418 38 59521 5 1.9 6.16 Ras-related protein O-Krev precursor gi|131854 49 21260 4 19.6 5.69 rCG51007 [Rattus norvegicus] gi|149016471 40 121602 2 1.9 8.9 Recombination activating protein 1 [Cardinalis cardinalis] gi|18845844 52 112115 2 1.4 8.47 Reticulon 4-C [Gallus gallus] gi|32331275 75 22279 4 7 9.18 Reticulon3 [Gallus gallus] gi|38605959 128 22091 7 12.9 6.36 Ribosomal protein 16S gi|200796 326 16460 17 31.7 10.21 Ribosomal protein L10a [Gallus gallus] gi|44967945 145 20956 8 25 9.67 Ribosomal protein L13 [Gallus gallus] gi|45384528 109 24438 7 16.1 11.75 Ribosomal protein L14 [Gallus gallus] gi|12381873 70 15639 6 35.9 10.55 Ribosomal protein L17 (L23) isoform 1 [Canis familiaris] gi|73969048 48 21613 5 18.5 10.07 Ribosomal protein L18 [Gallus gallus] gi|44968046 330 18895 17 30.1 11.84 Ribosomal protein L21 isoform 2 [Gallus gallus] gi|50731019 71 18622 5 28.8 10.49 Ribosomal protein L22 [Gallus gallus] gi|45383834 139 14777 12 32.8 9.21 Ribosomal protein L24 [Gillichthys mirabilis] gi|10121631 47 17813 4 14.1 11.46 Ribosomal protein L26 isoform 2 [Gallus gallus] gi|118097325 54 17248 6 23.4 10.55 Ribosomal protein L3 [Gallus gallus] gi|57525400 157 46342 12 18.6 10.2 Ribosomal protein L30 gi|17368239 155 13105 6 34.5 9.65 Ribosomal protein L35a (L32) gi|132942 77 12710 3 20 11.04 Ribosomal protein L4 [Gallus gallus] gi|44968095 230 31982 20 28.2 10.98 Ribosomal protein L5-A gi|132983 39 34312 2 10.8 9.66 Ribosomal protein L6 [Gallus gallus] gi|45383808 265 33902 13 16.4 10.67 Ribosomal protein L7 [Gallus gallus] gi|57530626 170 28819 20 30.9 10.83 Ribosomal protein L8 [Gallus gallus] gi|118083996 91 27166 5 14.5 11.12 Ribosomal protein L9 homologue [Gallus gallus] gi|50774641 88 21936 6 19.8 10.08 Ribosomal protein P0 (L10E) isoform 3 [Pan troglodytes] gi|114577027 116 34427 9 13.6 5.51 Ribosomal protein P0 [Gallus gallus] gi|45384494 388 34435 28 40.2 5.72 Ribosomal protein S12 [Rattus norvegicus] gi|109472521 49 14001 4 20.7 8.44 Ribosomal protein S15a [Rattus norvegicus] gi|109507837 110 14734 9 32.3 9.88 Ribosomal protein S17 (AA 7-135) [Gallus gallus] gi|63781 45 14885 2 9.3 9.64 Ribosomal protein S2 [Rattus norvegicus] gi|62655115 64 31251 4 4.5 9.85 Ribosomal protein S24 (S19) gi|133863 98 15274 4 20.5 10.71 Ribosomal protein S26 [Platichthys flesus] gi|12641796 59 6074 2 28.3 9.3 Ribosomal protein S3A [Gallus gallus] gi|129270064 235 30076 16 37.1 9.74 Ribosomal protein S4 [Xenopus tropicalis] gi|45360467 154 29831 10 20.2 10.16 Ribosomal protein S5 gi|133972 74 23035 4 11.3 9.68 Ribosomal protein S6 [Gallus gallus] gi|6601470 102 28577 4 10.1 10.83 Ribosomal protein S8 [Gallus gallus] gi|44968182 155 22113 16 41.8 10.18 Ribosomal protein SA isoform 2 [Gallus gallus] gi|50732898 359 33115 17 28 4.8 Rig homolog [human, brain, Peptide Partial, 135 aa] gi|262391 64 15802 2 9.6 10.41 RNA binding protein DEF-3 [Monodelphis domestica] gi|126335833 48 131336 2 1.2 6.21 Rps16 protein [Bos taurus] gi|76614740 140 16473 8 24.1 10.14 Saccharopine dehydrogenase (putative) [Gallus gallus] gi|61097999 581 47224 45 30.9 9.13 Selenoprotein N, 1 [Xenopus tropicalis] gi|116812916 47 64259 2 1.6 5.11 Smad3 [Equus caballus] gi|17736830 40 13915 3 6.5 4.96 SMC2 protein, partial [Bos taurus] gi|119921131 47 124407 2 0.8 8.29 SNAP gamma [Ornithorhynchus anatinus] gi|149411293 56 34861 3 2.6 5.44 Spectrin, beta, non-erythrocytic 1 [Gallus gallus] gi|118087525 83 274739 5 3.3 5.37 Statin-related protein gi|206440 328 50649 24 27.9 9.05 Stomatin (EPB72)-like 1 [Canis familiaris] gi|74000973 49 46291 2 1.8 8.86 Sulfotransferase 1C2 (SULT1C) (SULT1C#2) [Canis familiaris] gi|57092831 40 35610 2 4.3 6.87 Synaptobrevin SYBII gi|606978 39 9445 2 29.3 6.07 T19 protein [Ovis aries] gi|2578428 43 20935 2 3.7 4.28 TB2 gi|182403 35 22428 2 9.6 8.05 Testis expressed protein 14 [Gallus gallus] gi|118100294 47 119332 3 1.4 5.55 THY1 [Gallus gallus] gi|30316401 92 18391 6 15.6 7.6 -like [Danio rerio] gi|170015991 35 3223561 3 0.1 5.99 activator gi|292496 51 115343 3 0.9 8.72 Transducin beta chain 1 gi|62900169 39 38152 2 6.2 5.47 Transmembrane protein 33 [Homo sapiens] gi|8922491 50 28275 3 4.9 9.75 Troponin C-like protein gi|223036 179 16696 6 22.3 4.12 Ttranslocase of inner mitochondrial membrane 44 [Pan troglodytes] gi|114675079 41 78149 2 3.3 8.53 TUBB [Salmo salar] gi|148362136 203 50076 7 12.8 4.82 Tubulin beta [Cricetulus griseus] gi|49481 203 50109 8 16 4.85 Tyrosine kinase [Cubanichthys pengelleyi] gi|408421 39 11520 2 19.8 8.12 Unknown (protein for MGC:160678) [Xenopus laevis] gi|122936398 186 11531 13 29.1 11.33 Vacuolar protein sorting 35 [Gallus gallus] gi|57524880 42 92504 2 1.8 5.38 Valosin-containing protein [Homo sapiens] gi|6005942 77 89950 5 6 5.14 Variable lymphocyte receptor A diversity region [Petromyzon marinus] gi|126570400 38 25199 2 5.8 7.46 VARS2L protein variant [Homo sapiens] gi|62088538 42 185647 2 1 7.23 Vertebrate niban protein [Danio rerio] gi|56207511 41 79767 3 1.2 5.15 Vesicle amine transport protein 1 homolog (T californica) [Gallus gallus] gi|118103033 77 41993 4 11 6.18 WD repeat domain 17 isoform 1 [Monodelphis domestica] gi|126331215 56 144025 4 1.1 6.24 xylosylprotein beta 1,4-galactosyltransferase 7 isoform 3 [Macaca mulatta] gi|109079970 41 37905 3 2.4 8.69 Supplemental Table 5

Protein description Protein accession Protein score Protein mass Protein matches Protein cover Isoelectric point

Acetylcholinergic receptor M4 [Narudasia festiva] gi|156067640 46 16197 2 13.6 9.21 Acidic ribosomal phosphoprotein [Pagrus major] gi|37779102 125 23465 6 25.8 8.49 Aconitase 2, mitochondrial [Gallus gallus] gi|45383738 47 86535 4 7.8 8.05 Actin beta[Gallus gallus] gi|63018 554 42080 31 51.2 5.29 Actin-gamma like protein [Mus musculus] gi|6425087 498 44029 25 40.7 5.11 Actin, cytoplasmic (BfCA1) gi|3182905 311 41979 25 37.6 5.3 Actin, muscle gi|3182895 185 42361 18 29.1 5.23 Adenosine triphosphatase [Xenopus laevis] gi|148229987 720 114086 25 12.6 5.29 Solute carrier family 25 member 5, (Adenine nucleotide translocator 2) gi|113459 50 33102 2 4 9.76 AHNAK nucleoprotein, partial [Gallus gallus] gi|118129464 68 54492 4 11.1 5.19 Aldehyde dehydrogenase 3 family, member A2 [Gallus gallus] gi|57525324 84 54546 3 9.2 8.4 AM2 receptor [Mus musculus] gi|49942 51 523309 4 0.8 5.17 Annexin 1 gi|529725 83 17422 1 10.4 6.19 Annexin 11 [Gallus gallus] gi|61098342 101 39012 4 16.7 8.34 Annexin 2 [Gallus gallus] gi|45382533 542 38901 33 55.8 6.92 Annexin 5 gi|62738641 116 36159 16 41.3 5.61 Annexin 6 [Gallus gallus] gi|50982399 1091 75579 45 47.8 5.57 Annexin 8 VAC beta [Gallus gallus] gi|50749462 205 36938 8 20.5 5.24 AP-1 complex subunit beta-1 (Beta1-adaptin) (Beta-adaptin 1) gi|1703167 62 105452 1 1.6 4.94 AP-1 complex subunit gamma-1 (Adapter-related protein complex 1 subunit gamma-1) gi|113349 43 92147 3 4.6 6.36 AP-1, Adaptor-related protein complex mu subunit 1 [Mus musculus] gi|6671557 77 48683 1 3.3 6.82 AP-2, adaptor-related protein complex 2, beta 1 subunit isoform b [Homo sapiens] gi|4557469 94 105398 4 3.8 5.22 Atlastin [Gallus gallus] gi|118092343 42 63641 2 6.1 5.83 Bardet-Biedl syndrome 2 [Gallus gallus] gi|61098248 44 80484 2 1.8 5.42 Brain abundant, membrane attached signal protein 1 [Gallus gallus] gi|45383878 73 25423 2 14.3 4.66 BRI3 binding protein [Gallus gallus] gi|92110029 135 26810 3 8 8.97 Bromodomain adjacent to zinc finger domain, 1B [Monodelphis domestica] gi|126314430 43 172572 1 0.5 8.66 Ca2+-transporting ATPase (EC 3.6.3.8) RB5-10, brain - rat (fragment) gi|92028 42 10514 1 16.8 4.26 Calbindin 1, 28kDa [Gallus gallus] gi|45382893 48 30376 2 9.2 4.72 Calcyclin-associated protein, CAP50 gi|249043 42 2742 1 64 4.57 Calnexin [Gallus gallus] gi|71895293 382 68465 17 18.7 4.42 Calreticulin [Gallus gallus] gi|44969651 73 47079 8 18.6 4.41 CAMP responsive element binding protein 3-like 1 [Monodelphis domestica] gi|126332694 47 91825 1 1.3 5.8 Cancer susceptibility candidate 4 [Gallus gallus] gi|71895625 43 42642 2 3.7 5.79 [Gallus gallus] gi|50758260 49 151876 3 3.3 5.67 Carnitine O-acetyltransferase precursor (Carnitine acetylase) (CAT) gi|1705537 41 71592 3 3.7 8.65 Caspase 5 [Macaca mulatta] gi|109108505 39 45357 2 4.1 8.76 Cation-dependent mannose-6-phosphate receptor precursor [Gallus gallus] gi|118083280 123 33643 4 13.1 7.62 CENP-F kinetochore protein gi|924601 49 370674 2 0.7 5.03 open reading frame 3 [Gallus gallus] gi|57525135 66 46314 3 10.6 5.89 Clathrin heavy chain 1 [Homo sapiens] gi|4758012 260 193260 16 9.4 5.48 Claudin 3 [Gallus gallus] gi|46049089 49 23645 2 5.6 8.02 Claudin 8 [Bos taurus] gi|148235311 51 25077 2 5.3 8.72 Coatomer subunit alpha (Alpha-coat protein) (Alpha-COP) gi|1705996 71 139783 4 4 7.7 Coatomer subunit beta~ (Beta~-coat protein) (Beta~-COP) (p102) gi|544075 59 103153 2 2.1 5.15 Copper amine oxidase [Bos taurus] gi|119912472 43 75691 3 1.9 5.76 Cortactin-binding protein 2 (CortBP2) gi|90101864 41 181393 1 0.8 8.26 Creatine Kinase brain gi|6573489 329 42998 11 32.9 5.93 Cyclic AMP-regulated phosphoprotein, 21 kD [Ornithorhynchus anatinus] gi|149410059 46 26932 2 8.5 9.95 Cyclic-2~3, nucleotide 3~ phosphodiesterase [Gallus gallus] gi|45384252 54 47549 2 3.3 9.15 Cystatin C [Gallus gallus] gi|45382805 38 15562 2 12.2 7.6 Cytochrome b-5 [Gallus gallus] gi|48976095 152 15536 7 56.5 5.07 Cytochrome P450 family 17 polypeptide 2 [Oreochromis niloticus] gi|148612548 40 58166 2 1.7 8.35 DEAD box polypeptide 17 isoform 2 [Homo sapiens] gi|13787204 80 19246 3 8.2 9.71 Dedicator of cytokinesis protein 10 (Protein zizimin 3) [Rattus norvegicus] gi|109487395 42 271693 2 0.9 7.32 Diphthamide biosynthesis protein-2; DPH2 [Homo sapiens] gi|3170458 44 52457 2 2.5 5.25 DnaJ domain-containing protein RME-8 [Gallus gallus] gi|118085986 163 256634 11 6.7 6.35 Double substrate-specificity short chain dehydrogenase/reductase 2 [Gallus gallus] gi|50748322 61 36502 3 11 8.88 Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor Tu) (EF-Tu) gi|3122072 119 50467 11 18.6 9.1 Elongation factor 2 (EF-2) gi|119168 49 96304 2 3.7 6.31 Enolase alpha (2-phospho-D-glycerate hydro-lyase) (Tau-crystallin) gi|119338 78 47609 6 18.9 6.37 Eukaryotic translation elongation factor 1 alpha 2 [Xenopus tropicalis] gi|58332686 104 50775 8 16.8 9.1 Fibrous sheath CABYR binding protein [Bos taurus] gi|115496246 43 87878 2 1 4.02 FK506 binding protein 3, 25kDa [Gallus gallus] gi|46048916 61 25073 2 8.4 9.2 Flavin containing monooxygenase 6 [Gallus gallus] gi|45383027 64 61095 4 9.6 8.29 Fucosyltransferase 8 (alpha (1,6) fucosyltransferase) [Gallus gallus] gi|52345460 92 66763 5 13.4 6.57 G protein beta subuit like [Mus musculus] gi|475012 71 35453 2 8.8 8.08 Gelsolin [Gallus gallus] gi|45384386 145 86120 8 12.6 5.93 Globin beta [Homo sapiens] gi|4038415 88 6262 3 17.5 4.55 Globin D alpha [Gallus gallus] gi|63013 88 15770 3 22 7.01 Globin epsilon [Gallus gallus] gi|71895591 161 16469 13 40.8 9.2 Globin-A alpha gi|211114 139 15492 11 35.2 9.1 Glutamate dehydrogenase 1 [Bos taurus] gi|23306688 54 57972 3 7.9 7.03 Glutathione S-transferase [Gallus gallus] gi|50729056 218 17330 13 37.4 9.67 Glyceraldehyde-3-phosphate dehydrogenase gi|211797 1336 35989 56 54.7 8.71 Golgi apparatus protein 1 [Gallus gallus] gi|45382795 385 133560 23 16.9 6.47 Grb10 interacting GYF protein 1 [Mus musculus] gi|33943105 40 116464 2 0.7 5.32 GRP94 [Ornithorhynchus anatinus] gi|149637905 85 93693 7 8.5 4.84 GTP-binding protein gi|550062 159 23720 8 29.7 6.08 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (Transducin beta1) gi|3023838 131 38161 4 11.2 5.6 Guanine nucleotide-binding protein Gi2 alpha-subunit [Squalus acanthias] gi|6677598 110 40773 6 22 5.38 H+ transporting ATPase, mitochondrial F1 complex, alpha subunit [Gallus gallus] gi|45383566 66 60263 5 11 9.29 H+/K+ transporting ATPase, nongastric, alpha polypeptide [Monodelphis domestica] gi|126327532 55 116712 4 3.2 5.89 H+/K+-exchanging ATPase (EC 3.6.3.10) ATP1AL1 - human (fragment) gi|346261 53 10542 3 29 4.24 Heat shock 70kDa protein 5 precursor [Gallus gallus] gi|45382769 385 72088 21 31.4 5.12 Heat shock cognate 71 kDa protein gi|1346318 273 71524 15 13.9 5.19 Heat shock protein 90 [Dicentrarchus labrax] gi|37623887 82 83558 6 7.7 4.95 Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) gi|122609 253 16482 17 69.9 8.85 Hemoglobin subunit epsilon-M (Hemoglobin epsilon-M chain) (Epsilon-M-globin) gi|122724 40 16308 3 13.6 8.69 Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin) gi|232234 99 16192 6 12.9 6.58 Heterogeneous nuclear ribonucleoprotein H3 (2H9) [Gallus gallus] gi|60302824 66 36690 2 9.4 6.6 Heterogeneous nuclear ribonucleoprotein R isoform 2 [Homo sapiens] gi|5031755 58 71184 2 4.1 8.23 Hif1al2 protein [Danio rerio] gi|62203558 48 76065 2 1.7 6.38 High density lipoprotein binding protein [Homo sapiens] gi|4885409 47 141979 1 1.2 6.43 Hippocampus abundant transcript-like 1 [Equus caballus] gi|149757018 45 58264 2 6.6 5.24 Histone 1, H2ai (predicted) isoform 1 [Canis familiaris] gi|74003971 140 29091 6 12.7 10.68 Histone H2B [Bos taurus] gi|119900971 72 24347 3 7 9.98 Histone H4 [Bos taurus] gi|119930610 156 11794 11 50 11.22 Human P5 isoform 2 [Gallus gallus] gi|50745031 54 49157 4 16.3 5.02 Insulin-like growth factor 2 receptor [Gallus gallus] gi|45384454 113 282426 5 2.6 5.67 L-lactate dehydrogenase B chain (LDH-B) (Epsilon-crystallin) gi|126038 96 36523 2 5.1 7.07 Laminin-binding protein [Homo sapiens] gi|34234 50 31888 5 23.9 4.84 Lectin, mannose-binding, 1 [Gallus gallus] gi|71897199 37 56712 2 3.8 5.57 LIM and senescent cell antigen-like domains 1 [Homo sapiens] gi|169163572 40 66558 2 2.6 7.75 Lysosome-associated membrane glycoprotein 1 precursor (LAMP-1) gi|1346461 42 44215 1 1.7 6.24 Mitochondrial trifunctional protein, alpha subunit [Gallus gallus] gi|45384238 55 83818 3 6.1 9.19 MOB1 [Homo sapiens] gi|38194905 41 10552 3 12.1 9.34 Myelin basic protein [Gallus gallus] gi|45384134 115 18797 9 43.7 11.6 Myelin P0 protein precursor (Myelin protein zero) gi|585535 560 27621 40 33.3 9.59 Myosin heavy chain nonmuscle gi|212449 134 229866 8 4.7 5.42 Myosin, heavy polypeptide 9, non-muscle [Gallus gallus] gi|45382693 103 227446 5 3.1 5.47 N-ethylmaleimide-sensitive factor [Gallus gallus] gi|118102799 110 82638 4 8.1 6.38 Na+/K+ transporting ATPase alpha 4 [Equus caballus] gi|149755959 99 111895 6 4.7 5.64 Na+/K+ transporting ATPase, alpha 1 polypeptide [Gallus gallus] gi|45382945 955 113528 51 29 5.5 Na+/K+ transporting ATPase, alpha-3 (Sodium pump subunit alpha-3) gi|18202326 441 112860 16 9.2 5.36 Na+/K+ transporting ATPase, beta 4 polypeptide [Gallus gallus] gi|113206084 67 36852 5 10.9 7.98 NADH dehydrogenase subunit 2 [Thamnophis validus thamnophisoides] gi|16417572 42 38216 1 6.7 9.46 NADPH-cytochrome P450 [Gallus gallus] gi|118100147 78 77319 2 4.9 5.42 Neurofilament medium polypeptide (NF-M) (Neurofilament triplet M protein) (160 kDa) gi|128150 43 95848 1 1.2 4.77 Neuromedin-B receptor (NMB-R) (Neuromedin-B-preferring bombesin receptor) gi|128393 43 43995 1 5.1 8.93 Ninein gi|1113865 41 251410 1 0.6 4.98 Nucleobindin 2 [Gallus gallus] gi|57530004 78 53847 2 5.5 5.02 Otoferlin [Gallus gallus] gi|118089149 105 229785 7 3 5.62 Outer mitochondrial membrane cytochrome b5 [Gallus gallus] gi|71895491 141 16204 3 23.6 5 Oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) [Gallus gallus] gi|71897293 56 116305 3 2.8 6.56 splice [Gallus gallus] gi|118104279 65 137096 1 1.1 6.23 Pa2g4 protein [Xenopus laevis] gi|28422615 38 44477 2 7.1 7.25 Peptidylprolyl isomerase B (cyclophilin B) [Gallus gallus] gi|45382027 64 22456 5 23.2 9.4 Pgrmc2 protein [Xenopus tropicalis] gi|39794459 65 25054 2 6.3 4.85 Phosphoglycerate kinase [Macropus agilis] gi|2746056 84 10810 2 17 9.34 Phosphoglycerate mutase gi|189868 36 29003 2 5.5 9.01 Phosphohexose isomerase gi|225994 93 62917 2 5.2 7.75 Plasma membrane Ca2+ pumping ATPase gi|190133 41 135594 1 1.5 5.69 Polydom protein [Gallus gallus] gi|118104463 41 394025 1 0.9 9.99 Polypeptide N-acetylgalactosaminyltransferase 6 [Gallus gallus] gi|71896101 116 71527 3 4.5 7.26 Preproacrosin [Equus caballus] gi|149759321 47 48454 2 2.3 9.41 Probable ATP-dependent RNA helicase DDX46 (DEAD box protein 46) gi|75061689 37 117902 2 3.1 9.33 Proliferation-associated protein 1, partial [Gallus gallus] gi|118129651 52 38840 2 8.2 8.64 Prolyl-4-hydroxylase (AA 5 - 494) [Gallus gallus] gi|63739 58 55174 2 5.9 4.66 Protein 14-3-3, theta polypeptide [Homo sapiens] gi|5803227 48 28032 1 5.7 4.68 Protein disulfide isomerase-associated 3 precursor [Gallus gallus] gi|45383890 217 56546 10 23.6 5.76 Protein kinase, DNA-activated, catalytic polypeptide [Gallus gallus] gi|45382811 51 477303 2 0.2 7.09 Protein transport protein Sec24B (SEC24-related protein B) gi|13124510 87 138900 3 1 6.24 Protein transport protein Sec24C (SEC24-related protein C) gi|27735256 47 119779 3 2.7 6.71 [Gallus gallus] gi|45384124 97 30901 6 13.4 8.72 Proto-oncogene protein [Hydrobates pelagicus] gi|112950272 52 19239 3 6 9.27 Putative aldo-keto reductase family 1 member CL2 [Sus scrofa] gi|113205716 42 32853 1 4.9 6.67 Pyruvate kinase [Homo sapiens] gi|35505 172 58411 10 13.6 7.58 Pyruvate kinase, muscle [Gallus gallus] gi|45382651 385 58434 17 25.7 7.29 Rab GDI [Homo sapiens] gi|285975 72 51088 1 4.3 5.94 Rab-11B (ORA3) gi|131849 62 24654 3 11 5.64 Rab-1B gi|75077202 119 22356 9 29.4 5.93 Rab-related GTP-binding protein [Homo sapiens] gi|1491714 45 25253 2 5.1 6.9 RAB10, member RAS oncogene family [Mus musculus] gi|7710086 71 22755 7 22.5 8.59 RAB14, member RAS oncogene family [Rattus norvegicus] gi|16758368 52 24140 3 12.1 5.85 Rab15 protein [Mus musculus] gi|15489394 45 19558 5 13.1 5.93 RAB18, member RAS oncogene family [Mus musculus] gi|6755258 49 23306 2 14.1 5.24 RAB1A, member RAS oncogene family [Homo sapiens] gi|4758988 163 22891 12 37.1 5.93 RAB33B, member of RAS oncogene family [Mus musculus] gi|8394133 45 26206 2 4.8 7.62 RAB35, member RAS oncogene family [Homo sapiens] gi|5803135 45 23296 5 10.9 8.52 RAB4B protein [Homo sapiens] gi|45708726 65 13642 4 19.8 9.26 RAB5A, member RAS oncogene family [Gallus gallus] gi|57530730 48 23755 2 13 8.31 Rab5c-like protein gi|508285 48 23781 2 13 8.87 Rab7 [Mus musculus] gi|1050551 94 23829 4 13 7.53 Ral guanine nucleotide dissociation stimulator [Equus caballus] gi|149758418 50 59521 3 1.9 6.16 Ras-related protein O-Krev precursor gi|131854 168 21260 4 7.6 5.69 RBP-MS/type 5 [Homo sapiens] gi|1669555 42 10658 1 7.1 9.47 Receptor expression enhancing protein 5 [Gallus gallus] gi|118104241 49 33585 4 5.6 9.28 Rer1 [Homo sapiens] gi|3859980 41 23506 2 5.3 6.43 Reticulon 1 [Gallus gallus] gi|47825381 36 82623 2 2.8 4.76 Reticulon 3-w [Gallus gallus] gi|38605959 147 22091 8 21.8 6.36 Reticulon 4-C [Gallus gallus] gi|32331275 81 22279 3 7 9.18 Ribosomal protein gi|198578 58 17730 7 23.7 11.12 Ribosomal protein 16S gi|200796 163 16460 9 37.2 10.21 Ribosomal protein L10 (Jun-binding protein JIF-1) gi|1172808 82 24428 4 25.2 10.14 Ribosomal protein L11 [Homo sapiens] gi|495126 75 20331 3 7.9 9.6 Ribosomal protein L13 [Gallus gallus] gi|45384528 54 24438 2 10 11.75 Ribosomal protein L17 homolog [Dicentrarchus labrax] gi|4028025 212 15592 7 29.4 10.89 Ribosomal protein L18 [Gallus gallus] gi|44968046 61 18895 3 10.2 11.84 Ribosomal protein L22 [Gallus gallus] gi|45383834 100 14777 6 30.5 9.21 Ribosomal protein L23 gi|306549 46 16730 2 16.3 10.46 Ribosomal protein L26 gi|132827 57 17267 3 13.8 10.63 Ribosomal protein L3 [Bos taurus] gi|7159574 46 46267 2 5.5 10.2 Ribosomal protein L30 [Homo sapiens] gi|4506631 101 12947 5 34.8 9.65 Ribosomal protein L31 [Homo sapiens] gi|1655596 89 14084 3 21.5 10.54 Ribosomal protein L32 [Homo sapiens] gi|4506635 69 15964 2 9.6 11.32 Ribosomal protein L35 [Homo sapiens] gi|6005860 69 14543 3 18.7 11.04 Ribosomal protein L38 [Homo sapiens] gi|4506645 48 8270 2 17.1 10.1 Ribosomal protein L4 [Gallus gallus] gi|44968095 72 31982 5 17.1 10.98 Ribosomal protein L6 [Gallus gallus] gi|45383808 173 33902 4 12.8 10.67 Ribosomal protein L7 [Gallus gallus] gi|57530626 84 28819 12 32.1 10.83 Ribosomal protein L9 homologue [Gallus gallus] gi|50774641 66 21936 2 14.1 10.08 Ribosomal protein P0 [Gallus gallus] gi|45384494 83 34435 4 16.8 5.72 Ribosomal protein P1 isoform 1 [Homo sapiens] gi|4506669 67 11621 3 14 4.26 Ribosomal protein S10 [Canis familiaris] gi|73972594 36 49431 3 6.4 10.31 Ribosomal protein S11 [Homo sapiens] gi|4506681 64 18590 2 19.6 10.31 Ribosomal protein S12 gi|133742 47 14859 2 7.6 6.3 Ribosomal protein S13 [Homo sapiens] gi|553640 146 13313 8 29.3 10.59 Ribosomal protein S14 [Mus musculus] gi|3097244 65 16462 3 23.8 10.14 Ribosomal protein S15a [Rattus norvegicus] gi|109507837 73 14734 3 18.1 9.88 Ribosomal protein S17 (AA 7-135) [Gallus gallus] gi|63781 51 14885 3 17.1 9.64 Ribosomal protein S18 [Pagrus major] gi|37779106 46 16230 4 19.3 11.11 Ribosomal protein S19 [Homo sapiens] gi|4506695 99 16051 8 23.4 10.31 Ribosomal protein S20 [Gallus gallus] gi|118086993 96 17110 5 18 9.66 Ribosomal protein S23 [Homo sapiens] gi|3088342 88 6522 5 39 9.36 Ribosomal protein S25 [Homo sapiens] gi|4506707 77 13791 3 8.8 10.12 Ribosomal protein S27a [Mus musculus] gi|94400086 46 15111 2 9.8 9.43 Ribosomal protein S3A [Gallus gallus] gi|129270064 139 30076 8 27.3 9.74 Ribosomal protein S4 gi|227229 38 29892 3 13.7 10.21 Ribosomal protein S5 gi|550021 148 22934 9 18.6 9.59 Ribosomal protein SA isoform 2 [Gallus gallus] gi|50732898 50 33115 5 23 4.8 Rpl10a-prov protein [Gallus gallus] gi|50760435 127 24864 6 28.1 9.88 Rps16 protein [Bos taurus] gi|76614740 76 16473 5 29.7 10.14 Ryanodine receptor type 3 [Mustela vison] gi|1526615 37 555819 2 0.6 5.54 Saccharopine dehydrogenase (putative) [Gallus gallus] gi|61097999 751 47224 48 44.2 9.13 SEC22 vesicle trafficking protein homolog B [Gallus gallus] gi|71895247 61 24873 3 20 8.86 SEC23A (S. cerevisiae) [Gallus gallus] gi|50748450 270 87043 10 12.7 6.51 Sec24A protein [Gallus gallus] gi|50755154 111 120690 4 2.7 8.07 Serine/threonine protein kinase MST4 [Pan troglodytes] gi|114690199 39 63508 2 2.9 9.51 SNAP gamma [Ornithorhynchus anatinus] gi|149411293 44 34861 1 2.6 5.44 Solute carrier family 8 member 3 [Acris crepitans] gi|123965123 49 43066 2 4 5.41 Sortilin 1 [Ornithorhynchus anatinus] gi|149637449 53 83871 2 1.6 6.02 Spectrin alpha nonerythroid gi|179106 39 284905 3 1.9 5.22 Spir-2 protein [Mus musculus] gi|27151755 50 81470 2 1.3 7.19 Statin-related protein gi|206440 151 50649 8 16.8 9.05 Steroid dehydrogenase [Gallus gallus] gi|118091511 66 38677 2 4.3 9.31 Surfeit 4 [Gallus gallus] gi|45383444 46 30827 2 11.5 7.64 Synaptobrevin SYBII gi|606978 62 9445 1 29.3 6.07 Tectorin beta [Gallus gallus] gi|46195453 117 37617 2 6.7 8.15 Thioredoxin [Gallus gallus] gi|45382053 58 11978 2 12.4 5.1 THY1 [Gallus gallus] gi|30316401 108 18391 5 25 7.6 Trafficking protein particle complex 2 [Gallus gallus] gi|57525493 57 16473 2 10 6.03 Trafficking protein particle complex 3 [Gallus gallus] gi|56605900 64 20434 2 15.6 4.87 Transferrin receptor protein 1 (TfR1) gi|20140635 98 85890 6 6.7 5.52 Transmembrane 9 superfamily protein member 3 precursor [Gallus gallus] gi|118092737 39 65251 2 3.8 7.07 Transmembrane 9 superfamily protein member 4 [Danio rerio] gi|41055736 42 37122 1 6.1 5.59 Transmembrane emp24 domain-containing protein 10 [Gallus gallus] gi|57529934 97 25016 6 22.4 6.37 Transmembrane protein 33 [Homo sapiens] gi|8922491 61 28275 2 4.9 9.75 Triose Phosphate Isomerase gi|230359 108 26755 5 17 7.26 Triosephosphate isomerase [Anser anser] gi|34221745 137 22790 7 25.6 6.19 Troponin C-like protein gi|223036 113 16696 7 22.3 4.12 Truncated pol/envelope fusion protein [Danio rerio] gi|125804017 35 30849 3 2.2 6.2 Tubulin alpha [Homo sapiens] gi|37492 115 50810 6 18.2 5.02 Tubulin beta [Halocynthia roretzi] gi|2443346 204 50460 15 31.2 4.73 Tubulin isotype M-alpha-2 gi|202210 112 50818 6 18.2 4.94 Tumor necrosis factor type 1 receptor associated protein TRAP-1 - human gi|1082886 65 75694 2 2.1 8.43 Tumor-associated calcium signal transducer 1 [Gallus gallus] gi|60302776 51 35136 2 9.2 7.42 Ubiquitin gi|229532 91 8446 5 39.2 6.56 UDP-GalNAc:polypeptide N-acetylgalactosaminyl transferase [Gallus gallus] gi|118088237 191 65459 6 12.5 8.63 Unc-18 homologue [Mus musculus] gi|1944322 39 68058 1 1.9 6.62 Vacuolar H+ ATPase E1 [Gallus gallus] gi|57525423 45 26159 1 6.2 7.74 Vacuolar protein sorting 13B isoform 1 [Gallus gallus] gi|118087185 41 451737 1 0.3 5.91 Vacuolar protein sorting 13D [Gallus gallus] gi|118101204 43 488623 1 0.3 6.01 Vacuolar protein sorting 35 [Gallus gallus] gi|57524880 141 92504 8 10.2 5.38 Valosin containing protein [Danio rerio] gi|41393119 87 89995 5 5.3 5.14 VAMP (vesicle-associated membrane protein)-associated protein B and C [Gallus gallus] gi|57529406 100 27427 2 12.3 6.92 Vamp-associated protein, VAP-33 [Homo sapiens] gi|4191319 40 27528 2 11.6 8.8 Vesicle amine transport protein 1 homolog (T californica) [Gallus gallus] gi|118103033 39 41993 4 14.1 6.18 Voltage-dependent anion-selective channel protein 2 (VDAC-2) gi|11134020 54 30162 2 11.3 8.63 Williams-Beuren syndrome critical region protein 25 [Mus musculus] gi|94375490 42 30775 2 3 11.98 Xylulokinase homolog [Homo sapiens] gi|18860918 43 59086 2 2.4 5.55 Zinc finger protein [Ciona intestinalis] gi|93003164 42 161597 2 0.6 9.14 Zinc finger, CDGSH-type domain 2 [Gallus gallus] gi|50746903 160 15466 6 35.8 9.66 Supplemental Table 6

Protein description Protein acession Protein score Protein mass Protein matches protein coverage Isoelectric point

Acetylcholinergic receptor M4 [Narudasia festiva] gi|156067640 49 16197 3 13.6 9.21 Actin beta [Oncorhynchus mykiss] gi|7839450 475 38257 28 41.2 5.39 Actin-gamma like protein [Mus musculus] gi|6425087 604 44029 31 32.8 5.11 Actin, muscle-type (A2) gi|3121741 371 42521 27 30.7 5.12 Adenomatosis polyposis coli 2 [Canis familiaris] gi|73987556 40 272093 2 0.4 9.61 AHNAK nucleoprotein, partial [Gallus gallus] gi|118123583 67 80260 3 5.3 5.49 Annexin 1 gi|529725 51 17422 2 18.2 6.19 Annexin 11 [Gallus gallus] gi|61098342 153 39012 7 25.6 8.34 Annexin 2 [Gallus gallus] gi|45382533 534 38901 34 43.7 6.92 Annexin 5 gi|62738641 424 36159 26 43.4 5.61 Annexin 6 [Gallus gallus] gi|50982399 321 75579 21 24.9 5.57 Annexin 8, VAC beta [Gallus gallus] gi|50749462 351 36938 18 36.4 5.24 AP-1 complex subunit beta-1 (Adapter-related protein complex 1 subunit beta-1) gi|1703167 38 105452 1 1.6 4.94 Brain abundant, membrane attached signal protein 1 [Gallus gallus] gi|45383878 52 25423 2 5.7 4.66 BTB (POZ) domain containing 14A isoform 2 [Rattus norvegicus] gi|34853069 40 63811 2 1.9 5.73 Calbindin 1, 28kDa [Gallus gallus] gi|45382893 122 30376 7 23.7 4.72 Calcium binding protein [Gallus gallus] gi|50736185 48 20879 2 6.2 4.97 Calnexin [Gallus gallus] gi|71895293 71 68465 3 7.3 4.42 Calreticulin [Gallus gallus] gi|44969651 161 47079 11 20.8 4.41 Carbonate dehydratase, 2-phosphopyruvate-hydratase alpha-enolase [Homo sapiens] gi|693933 373 47421 15 22.1 7.01 Casein kinase 1, alpha 1-like [Homo sapiens] gi|21624639 44 39275 3 4.7 9.47 Catenin beta And Alpha gi|9955246 40 22429 2 3.9 8.76 Cation-dependent mannose-6-phosphate receptor [Gallus gallus] gi|118083280 71 33643 2 10.1 7.62 Chromosome 6 open reading frame 105 [Ornithorhynchus anatinus] gi|149638652 44 35188 2 3.3 10.34 Claudin 1 [Gallus gallus] gi|61889131 71 23011 3 5.7 8.85 Claudin 3 [Gallus gallus] gi|46049089 61 23645 5 10.3 8.02 Claudin 8 [Bos taurus] gi|148235311 52 25077 2 5.3 8.72 Coatomer protein complex, subunit alpha [Gallus gallus] gi|71897175 44 140060 5 4.4 7.53 Coatomer subunit beta~ (Beta~-coat protein) (Beta~-COP) (p102) gi|544075 62 103153 1 2.1 5.15 Coiled-coil-helix-coiled-coil-helix domain containing 2 [Mus musculus] gi|18079334 45 15879 2 8.5 9.78 Complement component 4 binding protein, alpha chain precursor [Gallus gallus] gi|45382791 45 50174 2 5.5 5.87 Copine III [Homo sapiens] gi|4503015 50 60947 2 3 5.6 Creatine Kinase brain gi|6573489 688 42998 37 50.8 5.93 Cytochrome b5 gi|226450 78 15450 5 38.2 4.9 Cytochrome P450 family 17 polypeptide 2 [Oreochromis niloticus] gi|148612548 39 58166 2 1.7 8.35 Defender against cell death 1 [Gallus gallus] gi|7021380 39 11499 2 11.3 8.76 Destrin isoform a [Homo sapiens] gi|5802966 58 18950 2 14.5 8.06 3 isoform 1 [Macaca mulatta] gi|109128973 38 57728 2 6.1 9.03 Diphthamide biosynthesis protein-2; DPH2 [Homo sapiens] gi|3170458 43 52457 2 2.5 5.25 Dynein heavy chain 7 [Canis familiaris] gi|73985341 41 463602 1 0.4 5.66 Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor Tu) (EF-Tu) gi|3122072 64 50467 6 13.4 9.1 Enolase 1 [Gallus gallus] gi|46048768 454 47617 21 34.1 6.17 Enolase A [Typhlonectes natans] gi|98979419 314 47637 12 19.1 6.53 Enolase alpha (2-phospho-D-glycerate hydro-lyase) (Tau-crystallin) gi|119338 435 47609 20 26.7 6.37 Enolase-1beta [Chiloscyllium punctatum] gi|11999263 211 39672 8 16 5.88 FAT tumor suppressor homolog 4 isoform 1 [Equus caballus] gi|149698234 39 545971 2 0.4 4.73 Flavin-containing monooxygenase 3 [Gallus gallus] gi|37931456 55 55696 2 4.8 8.65 Gelsolin [Gallus gallus] gi|45384386 54 86120 3 5 5.93 Glucose phosphate isomerase [Gallus gallus] gi|57524920 185 62405 9 19.7 7.4 Glutathione S-transferase [Gallus gallus] gi|50729056 139 17330 10 34.2 9.67 Glyceraldehyde-3-phosphate dehydrogenase gi|211797 938 35989 35 41.7 8.71 Glycoprotein [Sus scrofa] gi|4454998 44 11048 3 14.1 4.44 Golgi complex autoantigen golgin-97 isoform 1 [Ornithorhynchus anatinus] gi|149637111 67 88246 2 1.8 5.28 Grb10 interacting GYF protein 1 [Mus musculus] gi|33943105 40 116464 2 0.7 5.32 GRP94 [Ornithorhynchus anatinus] gi|149637905 135 93693 10 14.5 4.84 GTP-binding protein gi|550062 168 23720 9 22.2 6.08 Guanine nucleotide binding protein alpha oB isoform 6 [Gallus gallus] gi|118096242 57 40661 4 13 5.35 Guanine nucleotide-binding protein G(I)/G(S)/G(T) beta-1 (Transducin beta chain 1) gi|3023838 205 38161 12 27.6 5.6 H(+)/K(+) ATPase subunit alpha cytoplasmic non gastric gi|20137385 236 116245 17 5.3 5.37 H+ transporting, ATP synthase, mitochondrial F1 complex, beta subunit [Gallus gallus] gi|71897237 141 56650 8 17.4 5.59 Heat shock 70kDa protein 5 precursor [Gallus gallus] gi|45382769 129 72088 12 19.3 5.12 Heat shock protein 108K gi|211945 199 91835 14 17.6 4.86 Heat shock protein 70 cognate gi|309319 196 71021 16 21.4 5.37 Heat shock protein 90kDa alpha (cytosolic), class A member 1 [Gallus gallus] gi|157954047 97 84406 8 9.1 5.01 Hemoglobin subunit alpha globin D alpha [Gallus gallus] gi|63013 99 15770 4 22 7.01 Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) gi|399861 194 16496 13 45.9 8.85 Heparin-binding protein 15 - bovine gi|627739 57 14405 2 19.2 9.73 Histone H2A.2 [Homo sapiens] gi|31979 120 13898 5 28.6 10.21 Histone H4, partial [Bos taurus] gi|119930610 91 11794 7 39.6 11.22 Human P5 isoform 2 [Gallus gallus] gi|50745031 84 49157 5 7.4 5.02 Inhibitor of apoptosis protein 1 gi|1184316 69 69568 3 1.5 5.71 Inner-ear cytokeratin [Rana catesbeiana] gi|6980088 83 56584 3 4.5 5.81 Integrin, alpha 5 [Gallus gallus] gi|45382133 72 115457 2 3.4 5.42 Integrin, beta 1 [Gallus gallus] gi|86129418 52 91802 3 5.2 5.23 Integrin, beta 5 [Gallus gallus] gi|45383197 40 91612 1 2.1 6.31 Interleukin 13 receptor alpha 1 [Bos taurus] gi|119919617 40 50879 2 1.6 9.07 Killer cell immunoglobulin-like receptor [Ornithorhynchus anatinus] gi|149412118 50 68041 2 3 4.5 Kinesin family member 26A, partial [Ornithorhynchus anatinus] gi|149434706 43 123520 1 1.2 7.53 Lactate dehydrogenase B [Gallus gallus] gi|45383766 101 36694 10 28.8 7.07 Laminin, alpha 2 (merosin, congenital muscular dystrophy) [Gallus gallus] gi|118088564 45 354263 2 0.3 5.97 Lysosomal membrane glycoprotein A gi|212254 69 45205 1 2.9 6.79 M phase phosphoprotein, MPP1 gi|292329 39 66113 2 1.8 8.61 Malate dehydrogenase 1, NAD (soluble) [Gallus gallus] gi|57530355 47 36748 2 9 6.92 Microtubule-associated protein 4 [Monodelphis domestica] gi|126335906 42 157719 1 0.5 9.22 Mitochondrial F1-Atpase Complexed With Aurovertin B gi|1827809 58 55314 3 8.2 7.87 MOB1 [Homo sapiens] gi|38194905 57 10552 2 12.1 9.34 Multidrug resistance protein gi|307375 79 21710 4 7.9 5.84 Mutant cysteine-rich FGF receptor [Gallus gallus] gi|1480467 40 126226 4 4.5 6.53 Myelin basic protein [Gallus gallus] gi|45384134 50 18797 3 16.1 11.6 Myelin P0 protein precursor (Myelin protein zero) (MPP) gi|585535 159 27621 14 22.1 9.59 Myosin gi|531138 42 9580 1 17.2 6.07 Na-K-2Cl cotransporter 1 [Xenopus laevis] gi|147904042 110 127345 4 3.3 6.13 Na+-dependent glutamate/aspartate transporter [Gallus gallus] gi|8132399 75 24510 1 8.8 5.33 Na+/K+ transporting ATPase, alpha 1 polypeptide [Gallus gallus] gi|45382945 2697 113528 147 39.7 5.5 Na+/K+ transporting ATPase, beta 4 polypeptide [Gallus gallus] gi|113206084 249 36852 13 23.4 7.98 Natural killer cell enhancing factor isoform 4 [Gallus gallus] gi|50751518 85 22529 8 34.2 8.24 NmrA-like family domain containing 1 [Gallus gallus] gi|71897147 46 32726 2 9.1 7.77 Non-metastatic cells 2, protein (NM23B) expressed in [Gallus gallus] gi|45384260 46 17448 3 26.8 7.72 Nucleobindin 2 [Gallus gallus] gi|57530004 78 53847 3 4.8 5.02 Numa1 protein [Rattus norvegicus] gi|71051118 64 71467 2 2.2 9.52 Otoferlin [Gallus gallus] gi|118089149 245 229785 15 6.4 5.62 Oxysterol binding protein-like 6, [Danio rerio] gi|125825332 41 108522 2 1.5 7.59 P300/CBP-associated factor [Bos taurus] gi|119887282 40 95691 1 1.2 9.04 Peptidylprolyl isomerase A-like, [Monodelphis domestica] gi|126303437 46 18204 2 14 7.64 Peptidylprolyl isomerase B (cyclophilin B) [Gallus gallus] gi|45382027 84 22456 3 13 9.4 Pericentrin (kendrin) [Macaca mulatta] gi|109065048 47 298034 2 0.3 5.64 Phosphatidylethanolamine-binding protein 1 (PEBP-1) [Gallus gallus] gi|50756703 69 21115 3 18.2 6.96 Phosphoglycerate kinase 1 [Gallus gallus] gi|45384486 90 45087 4 12.7 8.31 Phosphoglycerate mutase 1 (brain) [Gallus gallus] gi|71895985 63 29051 5 18.1 7.03 Plasma membrane Ca2+ pumping ATPase gi|190133 70 135594 3 4.3 5.69 Ppar Gamma gi|5107774 86 30833 3 3.7 5.76 Preproacrosin [Equus caballus] gi|149759321 50 48454 3 2.3 9.41 Pro-enkephalin gi|1093055 54 18589 2 11.8 5.14 Prolactin family 8, subfamily a, member 7 [Rattus norvegicus] gi|11968128 41 27652 2 5.8 5.83 Prolyl-4-hydroxylase (AA 5 - 494) [Gallus gallus] gi|63739 163 55174 9 15.7 4.66 Protein 14-3-3 [Homo sapiens] gi|5803227 110 28032 5 16.7 4.68 Protein disulfide isomerase family A, member 4 [Gallus gallus] gi|57530768 93 71285 5 7.5 4.96 Protein disulfide isomerase-associated 3 precursor [Gallus gallus] gi|45383890 198 56546 15 25.3 5.76 Protein kinase C inhibitor protein-1 epsilon isoform, 14-3-3 protein gi|249996 52 17714 4 29.6 5.12 Protein PP4-X gi|189617 87 36262 2 5 5.65 Proto-oncogene protein [Hydrobates pelagicus] gi|112950272 49 19239 2 6 9.27 Pyruvate kinase, muscle [Gallus gallus] gi|45382651 403 58434 25 33.4 7.29 Rab GDI [Homo sapiens] gi|285975 113 51088 3 8.5 5.94 Rab-10 (ORA1) gi|131847 64 22837 6 18.5 8.26 Rab-related GTP-binding protein [Homo sapiens] gi|1491714 58 25253 3 5.1 6.9 RAB11B, member RAS oncogene family [Canis familiaris] gi|73987203 96 45774 4 8.3 10.62 RAB14, member RAS oncogene family [Rattus norvegicus] gi|16758368 58 24140 5 15.8 5.85 Rab15 protein [Mus musculus] gi|15489394 57 19558 5 13.1 5.93 RAB1A, member RAS oncogene family [Homo sapiens] gi|4758988 212 22891 13 32.7 5.93 RAB33B, member of RAS oncogene family [Mus musculus] gi|8394133 58 26206 3 4.8 7.62 RAB35, member RAS oncogene family [Homo sapiens] gi|5803135 57 23296 5 10.9 8.52 RAB4B protein [Homo sapiens] gi|45708726 94 13642 6 19.8 9.26 Rab7 [Mus musculus] gi|1050551 109 23829 7 18.4 7.53 Rap1b gi|595280 44 21201 2 14.1 5.37 RAS viral (r-ras) oncogene homolog 2 [Gallus gallus] gi|57530014 65 23508 2 5.9 5.74 Receptor expression enhancing protein 5 [Gallus gallus] gi|118104241 56 33585 2 3.3 9.28 Recombination activating gene 1 [Paroedura bastardi] gi|155970031 46 36284 2 3.9 9.33 Regulated in COPD kinase transcript [Equus caballus] gi|149730546 37 150066 2 0.8 6.35 Reticulon 3w [Gallus gallus] gi|38605959 81 22091 3 12.9 6.36 Reticulon 4-C [Gallus gallus] gi|32331275 47 22279 1 7 9.18 Reverse transcriptase [Ciona intestinalis] gi|34392547 47 172585 2 0.6 9.69 Ribosomal protein L18 [Gallus gallus] gi|44968046 64 18895 2 18.1 11.84 Ribosomal protein L26 gi|132827 38 17267 2 6.2 10.63 Ribosomal protein L30 [Homo sapiens] gi|4506631 89 12947 3 24.3 9.65 Ribosomal protein L7 [Gallus gallus] gi|57530626 42 28819 4 13.4 10.83 Ribosomal protein S20 [Pelodiscus sinensis] gi|86355133 43 13465 2 19.3 9.95 Roundabout 1 [Gallus gallus] gi|118083736 41 186381 1 0.6 5.64 Saccharopine dehydrogenase (putative) [Gallus gallus] gi|61097999 544 47224 36 38.2 9.13 SEC14-like protein 1 [Rattus norvegicus] gi|109487759 41 79700 2 1.3 6.03 SEC22 vesicle trafficking protein-like 1 [Mus musculus] gi|6755448 51 24896 4 25.1 8.67 Smad3 [Equus caballus] gi|17736830 43 13915 2 6.5 4.96 Smoothelin-C [Gallus gallus] gi|8926310 43 50361 2 2 9.39 SNAP gamma [Ornithorhynchus anatinus] gi|149411293 46 34861 2 2.6 5.44 Solute carrier family 1 member 3, EAAT1, GLAST-1 gi|232176 75 59830 1 3.7 8.51 Solute carrier family 12 member 2 (Basolateral Na-K-Cl symporter) gi|1709293 78 131666 4 2.8 6.8 Sorcin [Gallus gallus] gi|124249424 38 22208 2 15.7 5.37 Spectrin V beta [Pan troglodytes] gi|114605005 38 11770 1 21.9 6.82 Spir-2 protein [Mus musculus] gi|27151755 82 81470 2 1.3 7.19 Supervillin [Equus caballus] gi|149743647 42 264005 1 0.6 6.65 Synaptobrevin SYBII gi|606978 39 9445 2 29.3 6.07 Synaptogyrin 1a [Monodelphis domestica] gi|126339512 36 25802 1 9.5 4.41 Synaptojanin 1 [Lampetra fluviatilis] gi|9937209 39 143027 1 1.8 6.12 Synaptotagmin VIIgamma [Equus caballus] gi|149725300 41 84184 1 1.3 9.63 Syntaphilin gi|21362912 38 58752 1 5.8 5.65 Syntaxin 8 [Gallus gallus] gi|71897371 48 26928 1 7.6 5.56 TBC1 domain family, member 21 [Canis familiaris] gi|74000971 39 38760 2 2.1 5.72 Tectorin beta [Gallus gallus] gi|46195453 70 37617 3 6.7 8.15 Tektin 2 (testicular) [Ornithorhynchus anatinus] gi|149638496 43 50016 2 3.7 5.76 Thioredoxin [Gallus gallus] gi|45382053 51 11978 2 12.4 5.1 Thioredoxin peroxidase [Homo sapiens] gi|5453549 66 30749 2 6.6 5.86 THY1 [Gallus gallus] gi|30316401 88 18391 5 15.6 7.6 Transmembrane emp24 domain-containing protein 10 [Gallus gallus] gi|57529934 76 25016 3 10.5 6.37 Transmembrane emp24 domain-containing protein 2 precursor gi|1352660 48 22289 3 10.7 5.07 Transmembrane emp24 protein transport domain containing 4 [Mus musculus] gi|19527236 51 26233 2 11.5 8.33 Transmembrane tight junction protein claudin [Xenopus laevis] gi|12004995 44 23763 2 6.1 8.49 TRIM5/cyclophilin A fusion protein [Aotus trivirgatus] gi|50301248 37 54865 2 5.3 6.72 Triose Phosphate Isomerase gi|230359 176 26755 9 27.5 7.26 Troponin C-like protein gi|223036 78 16696 2 22.3 4.12 Tubulin alpha [Homo sapiens] gi|37492 205 50810 10 28.2 5.02 Tubulin beta chain (Beta-tubulin) gi|18202612 193 50200 10 20.9 4.79 Tubulin, beta 5 [Mus musculus] gi|7106439 217 50095 14 34 4.78 Tubulin, beta 6 [Mus musculus] gi|27754056 192 50514 8 12.1 4.8 Tumor necrosis factor type 1 receptor associated protein TRAP-1 - human gi|1082886 61 75694 2 2.1 8.43 Tumor-associated calcium signal transducer 1 [Gallus gallus] gi|60302776 117 35136 8 18.6 7.42 Ubiquitin gi|229532 37 8446 4 51.4 6.56 Valosin-containing protein [Homo sapiens] gi|6005942 71 89950 5 4.6 5.14 VAMP-associated protein B/C [Homo sapiens] gi|4759302 58 27439 1 5.3 6.85 Vertebrate vasodilator-stimulated phosphoprotein (VASP) [Danio rerio] gi|169145928 36 15798 2 22 6.64 Vesicle amine transport protein 1 homolog (T californica) [Gallus gallus] gi|118103033 70 41993 2 2.9 6.18 Voltage-dependent anion-selective channel protein 2 (VDAC-2) gi|11134020 111 30162 3 13.8 8.63 Voltage-dependent calcium channel subunit alpha 1A [Bos taurus] gi|10178648 52 12761 2 13.6 6.96 Xylulokinase homolog [Homo sapiens] gi|18860918 45 59086 2 2.4 5.55 Zinc finger, CDGSH-type domain 2 [Gallus gallus] gi|50746903 95 15466 5 30.6 9.66 Supplemental Table 7

Protein description Accession number Protein score Protein mass Protein matches Protein coverage Isoelectric point

Acetylcholinergic receptor M4 [Narudasia festiva] gi|156067640 46 16197 2 13.6 9.21 Actin alpha 1 skeletal muscle protein [Homo sapiens] gi|169213772 105 51513 8 2.6 6.07 Actin cytoplasmic [Lethenteron japonicum] gi|13699190 1359 42137 96 58.5 5.3 Actin muscle [Lethenteron japonicum] gi|11875065 746 42423 74 36.3 5.23 Actin-beta gi|157878210 1557 41895 110 63.1 5.22 Actin-gamma like protein [Mus musculus] gi|6425087 1223 44029 76 44.5 5.11 Actin-like protein [Homo sapiens] gi|62421146 39 11780 2 14.6 6.63 Actin, muscle-type (A2) gi|3121741 1273 42521 90 44.4 5.12 Acyl-Coenzyme A thioesterase 2, mitochondrial [Rattus norvegicus] gi|62078649 46 50753 3 2.7 8.8 Adenine nucleotide translocase [Xenopus tropicalis] gi|45360469 1317 33335 57 37.6 9.76 Adenomatosis polyposis coli 2 [Canis familiaris] gi|73987556 46 272093 3 0.4 9.61 Adenosine A3 receptor [Eptesicus fuscus] gi|140429396 40 13365 3 8 9.04 Adenosine deaminase, RNA-specific, B2 [Homo sapiens] gi|8922077 42 81255 2 0.9 10.19 Adenosine triphosphatase isoform 2 [Gallus gallus] gi|118082377 238 135386 6 3.5 5.76 Adp-Ribose Pyrophosphatase Nudt9 gi|37927771 39 33020 2 4.8 6.16 Adp-Ribosylation Factor 1 Complexed With Gdp, Full Length Non-Myristoylated gi|1065361 181 20610 12 17.8 6.36 ALS2 [Gallus gallus] gi|118093428 45 184236 3 0.8 5.75 Amino acid starvation-induced protein gi|202990 56 13979 2 13.3 9.97 Amotl2 protein [Gallus gallus] gi|118094902 44 72961 2 1.1 6.99 Amyotrophic lateral sclerosis 2 (juvenile), partial [Ornithorhynchus anatinus] gi|149571431 48 100987 4 1.2 6.32 Anaphase-promoting complex subunit 8 [Homo sapiens] gi|6180017 39 69100 3 1.9 6.59 Ankyrin [Rattus norvegicus] gi|1841966 40 90326 1 2.7 8.07 Annexin 11 (Calcyclin-associated annexin 50) (CAP-50) gi|2492907 100 54419 5 1.8 7.53 Annexin 2 [Gallus gallus] gi|45382533 539 38901 22 19.8 6.92 Annexin 4 protein isoform 1 [Equus caballus] gi|149727504 84 36272 4 5 5.72 Annexin 5 gi|62738641 409 36159 32 26.6 5.61 Annexin 6 [Gallus gallus] gi|50982399 1406 75579 62 48.2 5.57 Annexin 8 VAC beta [Gallus gallus] gi|50749462 247 36938 12 24.5 5.24 Apolipoprotein B [Macroscelides proboscideus] gi|31558962 41 37678 2 2.7 9.11 Arachidonate 12-lipoxygenase isoform 1 [Canis familiaris] gi|73955347 42 76268 4 1.8 6.28 Arginine methyltransferase 7 CG9882-PA [Rattus norvegicus] gi|109507968 39 94902 2 1.5 5.14 Aristaless 3 [Canis familiaris] gi|73959917 48 48389 3 1.6 10.51 Aspartate aminotransferase (Glutamate oxaloacetate transaminase 2)(FABP-1) gi|112982 207 44938 7 7.5 9.04 ATP synthase alpha subunit, partial [Gallus gallus] gi|118103425 2350 42433 126 39 9.19 ATP synthase beta chain, mitochondrial precursor isoform 1 [Canis familiaris] gi|73968432 3365 56250 184 53.5 5.21 ATP synthase F0 subunit 6 [Gallus gallus] gi|5834849 73 24838 4 6.2 9.43 Atp5l protein [Gallus gallus] gi|118101946 122 17118 8 14.4 9.86 Biliverdin reductase A [Xenopus tropicalis] gi|55741962 42 32945 2 3.1 6.43 Bovine F1-Atpase Inhibited By Dccd (Dicyclohexylcarbodiimide) gi|11514059 3293 51655 179 56.6 5.03 Bradykinin B2 receptor gi|685244 40 42467 3 2.2 8.89 Brain protein [Homo sapiens] gi|6760015 43 37674 2 4.4 6.99 Brain-specific phosphatidic acid phosphatase-like protein 1 [Danio rerio] gi|125853797 36 83316 2 4.6 9.38 BRCA1 associated protein-1 [Homo sapiens] gi|4757836 48 80768 2 1.1 6.38 Calcium binding protein P22 [Homo sapiens] gi|6005731 52 22442 3 6.2 4.98 Calcium-Calmodulin N-Terminal Domain gi|16974825 45 8483 2 17.1 3.9 Calmodulin regulated spectrin-associated protein 1-like 1 [Homo sapiens] gi|44955929 72 167826 11 0.9 6.28 Calnexin [Gallus gallus] gi|71895293 447 68465 25 20.2 4.42 Calreticulin [Gallus gallus] gi|44969651 112 47079 17 18.8 4.41 CaM kinase-like vesicle-associated protein gi|82249010 37 47697 1 8.6 7 Carotene-9,10-monooxygenase, partial [Ornithorhynchus anatinus] gi|149480289 46 21339 3 4.3 8.39 Catenin beta and Alpha- gi|9955246 37 22429 5 3.9 8.76 CCAAT displacement protein, CDP [human, Peptide, 1505 aa] gi|300300 42 164710 2 0.7 5.83 CENP-F kinetochore protein gi|924601 47 370674 3 0.4 5.03 Chondroitin sulfate proteoglycan core protein [Gallus gallus] gi|1699007 42 225341 2 0.7 4.27 Chromosome 3 open reading frame 28 [Gallus gallus] gi|118083318 100 18955 3 9.1 10.07 Chromosome 6 open reading frame 152 [Equus caballus] gi|149722755 45 80635 3 1.7 8.38 Chymodenin gi|227130 71 10247 7 22.4 8.78 Citrate synthase, mitochondrial precursor gi|116243059 63 52198 8 4.9 8.65 Citrin; adult-onset type II citrullinemia protein [Equus caballus] gi|149705965 119 74356 9 8.5 8.79 Clathrin heavy chain 1 [Homo sapiens] gi|4758012 293 193260 14 6.9 5.48 Claudin 3 [Gallus gallus] gi|46049089 45 23645 5 9.8 8.02 Coagulation factor C homolog, cochlin (Limulus polyphemus) [Gallus gallus] gi|45384390 87 60016 10 19 8.61 Coilin [Mus musculus] gi|56206637 38 62392 1 6.7 9.13 Collagen Type I. Molecule gi|109156929 43 95928 3 1.8 6.59 COMM domain-containing 5 [Xenopus borealis] gi|183212081 68 22109 4 6.2 8.83 Complement component 8, gamma polypeptide [Monodelphis domestica] gi|126302813 73 72416 9 1.7 10 Creatine Kinase brain gi|6573489 1014 42998 72 52.1 5.93 Cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) [Xenopus tropicalis] gi|183986687 41 18704 2 6 6.05 Cytochrome b-5 reductase [Gallus gallus] gi|50729140 47 34295 3 4.3 8.7 Cytochrome b5 gi|226450 75 15450 3 35.3 4.9 Cytochrome c oxidase subunit II [Gallus gallus] gi|5834847 1188 25723 44 37 4.57 Cytochrome c oxidase subunit IV precursor [Gallus gallus] gi|71895513 239 19676 12 38.6 8.91 Cytochrome c oxidase subunit VIa [Gallus gallus] gi|50756677 241 11922 11 27.8 9.44 Cytochrome c reductase ubiquinol[Gallus gallus] gi|118098350 106 48777 10 15.3 9.04 Dermatan sulfate proteoglycan 3 precursor [Gallus gallus] gi|52138667 40 36176 2 3.5 4.8 Dihydrolipoamide dehydrogenase [Gallus gallus] gi|71897021 84 54568 4 4.7 8.19 Dihydrolipoamide S-acetyltransferase [Gallus gallus] gi|118102025 100 72561 4 9.1 8.84 DNA ligase IV [Xenopus tropicalis] gi|62859221 42 105173 3 0.9 7.53 DNA methyltransferase 1 [Mus musculus] gi|1765919 42 185624 2 0.5 8.37 DNA topoisomerase II binding protein 1 (TopBP1) [Canis familiaris] gi|73990583 55 191602 5 0.9 8.04 DnaJ subfamily A member 2-like [Danio rerio] gi|47086707 40 46178 4 2.7 5.83 Early mitotic inhibitor alpha [Xenopus borealis] gi|183212129 39 3951 2 34.3 9.75 Echinoderm microtubule associated protein like 3 [Danio rerio] gi|125820700 51 83193 1 1.6 6.39 Electron transfer flavoprotein, alpha polypeptide [Gallus gallus] gi|71895681 66 36999 2 8.1 8.87 ELG protein [Gallus gallus] gi|61098324 54 68798 2 2 5.62 Elongation factor 2 (EF-2) gi|119168 77 96304 4 5.2 6.31 Elongation Factor TuTS COMPLEX gi|56967054 43 45114 2 2.4 6.2 Elongin A2 [Macaca mulatta] gi|109122103 40 84662 2 0.8 9.58 Endonuclease G [Rattus norvegicus] gi|77917570 45 32362 2 3.4 9.54 Enhancer of zeste homolog 1 (ENX-2) [Gallus gallus] gi|118103040 41 87616 2 1.1 8.18 Enolase 1 [Gallus gallus] gi|46048768 101 47617 11 21.4 6.17 Enolase alpha [Bos taurus] gi|4927286 57 47589 7 15.9 6.44 Epsilon-globin [Elephantulus intufi] gi|71066838 62 9585 7 29.9 9.17 Erbb2-interacting protein ERBIN [Gallus gallus] gi|118103834 41 158075 1 0.7 5.44 ETS translocation variant 3 (ETS domain transcriptional repressor PE1) gi|62512143 38 57251 3 1.6 8.73 Eukaryotic translation initiation factor 2 alpha kinase PEK [Homo sapiens] gi|7341091 40 126118 2 0.7 5.32 Excision repair cross-complementing rodent repair deficiency [Homo sapiens] gi|4557563 40 90019 2 1.2 6.83 F-box and leucine-rich repeat protein 18 [Rattus norvegicus] gi|109476680 39 89782 2 1.9 8.62 Fatty acid binding protein 3 [Gallus gallus] gi|71894843 38 14807 2 15.8 5.92 FER-1-like protein 5 [Homo sapiens] gi|42558478 41 244338 1 0.6 7.84 Fibroblast growth factor receptor 1 IIIb VT- isoform [Oryzias latipes] gi|133740938 43 91856 2 1.5 6.27 Fibronectin type III domain containing 3B isoform 1 [Canis familiaris] gi|74003649 53 134875 1 2.7 5.68 FMRP Interacting Protein 82-Kda [Canis familiaris] gi|73967269 42 76794 3 1.7 8.71 Fumarase precursor (EC 4.2.1.2) gi|182794 49 50524 3 5.3 7.23 FYVE-finger-containing Rab5 effector protein Rabenosyn-5 [Homo sapiens] gi|11344951 43 89545 1 0.9 5.36 Gap junction protein, beta 6 [Gallus gallus] gi|45384376 264 31530 9 9.5 8.84 GekBS039P isoform 2 [Gallus gallus] gi|50755204 84 13073 8 23.9 9.15 Gelsolin [Gallus gallus] gi|45384386 184 86120 14 14 5.93 Giantin [Homo sapiens] gi|405715 38 377273 3 0.4 4.95 Globin alpha 1 [Gallus gallus] gi|52138655 1592 15533 55 63.4 8.54 Globin beta [Homo sapiens] gi|4038415 96 6262 3 17.5 4.55 Glucokinase (Hexokinase-4) (Hexokinase type IV) (HK IV) (HK4) (Hexokinase-D)gi|123902 44 52767 2 4.7 5.14 Glucose-regulated protein 78kDa [Oncorhynchus mykiss] gi|60223019 397 69907 45 30.6 5.02 Glutathione S-Transferase gi|2981970 67 25916 2 7.8 7 Glyceraldehyde-3-phosphate dehydrogenase gi|211797 1494 35989 68 41.7 8.71 GPR158-like 1 receptor [Bos taurus] gi|119912217 41 263200 2 1.1 5.56 GRP94 [Ornithorhynchus anatinus] gi|149637905 452 93693 32 21.4 4.84 GTP-binding protein gi|550062 69 23720 3 13.2 6.08 GTPase activating protein [Homo sapiens] gi|6759255 40 71640 3 1.9 9.08 H(+)/K(+) ATPase subunit alpha) gi|114343 752 115675 32 6.5 5.58 H+ transporting ATP synthase, mitochondrial F0 complex, subunit d [Gallus gallus]gi|50745451 584 18332 44 70.8 8.73 H+ transporting ATP synthase, mitochondrial F1 complex, beta subunit [Gallus gallus]gi|71897237 5125 56650 234 64.9 5.59 H+,K+-ATPase non-gastric [Monodelphis domestica] gi|126327528 400 123235 26 4.2 5.63 Heat shock 10kDa protein 1 [Gallus gallus] gi|45384204 101 11133 7 37.3 8.68 Heat shock 70kDa protein 5 precursor [Gallus gallus] gi|45382769 960 72088 79 52.5 5.12 Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8) [Canis familiaris]gi|74008507 181 44233 18 23.4 5.33 Heat shock protein 84b, partial [Ornithorhynchus anatinus] gi|149525990 177 91062 16 10.4 5.1 Heat shock protein 90kDa beta (Grp94), member 1 [Gallus gallus] gi|45383562 618 91726 38 24.8 4.83 Heat shock-induced protein [Monodelphis domestica] gi|126309577 118 70633 14 6.4 5.59 Hemoglobin D gi|4699641 957 16496 58 76 8.85 Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) gi|122708 809 16436 36 40.4 8.85 Hepatitis C virus core-binding protein 6 [Gallus gallus] gi|50745672 59 16427 2 9.9 9.71 Heterochromatin protein 1, binding protein 3 [Rattus norvegicus] gi|40018592 46 61054 2 2.2 9.69 Heterogeneous nuclear ribonucleoprotein R isoform 2 [Homo sapiens] gi|5031755 46 71184 2 2.1 8.23 Hexokinase 1 [Gallus gallus] gi|45383904 340 103847 32 21.4 6.32 High density lipoprotein binding protein [Homo sapiens] gi|4885409 53 141979 2 2.6 6.43 Histone 1, H1c [Gallus gallus] gi|95772089 44 22514 3 14.7 10.96 Histone H2A.2 [Homo sapiens] gi|31979 86 13898 4 17.5 10.21 Histone H4, partial [Bos taurus] gi|119930610 226 11794 16 37.7 11.22 Homeo box D10a [Danio rerio] gi|18858857 39 39432 2 6.1 9.06 Homeodomain protein [Equus caballus] gi|149703161 47 62158 2 1.4 10.86 Homer protein homolog 2 (Homer-2) (Cupidin) [Macaca mulatta] gi|109133494 41 23688 1 12.4 7.75 Homodimeric Agglutinin From Chicken Liver gi|7245936 109 14892 10 29.5 5.06 Homology to rat ribosomal protein L23 gi|306549 37 16730 2 8.8 10.46 HOXA13 [Leiocephalus barahonensis] gi|76363922 55 14530 3 27.5 5.89 Human P5 isoform 2 [Gallus gallus] gi|50745031 96 49157 5 12.8 5.02 Huntingtin [Danio rerio] gi|18858575 44 350725 2 0.4 5.72 Hydroxyacyl-Coenzyme A dehydrogenase [Danio rerio] gi|51011113 41 33430 2 7.1 8.66 Hydroxybutyrate-3 dehydrogenase [Gallus gallus] gi|57529615 64 38611 4 11.8 8.37 Hydroxyisobutyryl-3 Coenzyme A hydrolase, partial [Ornithorhynchus anatinus] gi|149588500 85 25381 7 5.2 10.15 Hydroxytryptamine-5 receptor 4 [Equus caballus] gi|32765778 46 14339 4 8.2 9.24 Hypoxia up-regulated 1 [Gallus gallus] gi|57528712 43 112534 2 3.3 5.14 Inhibitor of apoptosis protein 1 gi|1184316 45 69568 5 1.5 5.71 Inner-ear cytokeratin [Rana catesbeiana] gi|6980088 86 56584 2 4.5 5.81 Inter-alpha (globulin) inhibitor H4 [Monodelphis domestica] gi|126336622 58 101967 5 0.9 5.61 Ionotropic Glutamate Receptor-Like Glurdelta2 gi|157836482 51 29864 4 5.3 5.15 Kainate binding protein [Gallus gallus] gi|45382513 41 54891 1 4.3 8.24 Killer cell immunoglobulin-like receptor [Ornithorhynchus anatinus] gi|149412118 92 68041 9 10.4 4.5 Kinase anchoring protein 220 [Bos taurus] gi|119904455 44 217882 2 0.6 5.06 Kinase anchoring protein AKAP [Mesocricetus auratus] gi|13878279 41 91558 2 1.6 6.52 Kinectin gi|34098395 39 153839 1 1.4 5.52 Kinesin family member 20A [Gallus gallus] gi|61098268 41 100161 1 3.2 6.15 L-lactate dehydrogenase B chain (LDH-B) (Epsilon-crystallin) gi|126038 124 36523 5 18 7.07 Laminin, gamma 2 [Rattus norvegicus] gi|109498028 41 145271 1 2.6 6.08 LEK1 [Mus musculus] gi|6319178 55 284297 2 0.5 4.94 Lipid phosphate phosphatase-related protein type 2 [Homo sapiens] gi|12232395 41 37506 1 2.3 9.64 Low density lipoprotein-related protein 1 [Gallus gallus] gi|45382557 77 525788 1 0.4 5.05 Lsm4 protein [Takifugu rubripes] gi|13161882 42 16186 2 7.6 9.96 Malate dehydrogenase 2, NAD (mitochondrial) [Gallus gallus] gi|50758110 657 37401 40 45.6 8.83 Mannose-6-phosphate receptor binding protein 1, partial [Pan troglodytes] gi|114674769 45 34937 2 2.8 6.04 MDH2 protein [Equus caballus] gi|149756044 529 47167 26 22.3 9.64 Megakaryocyte stimulating factor; MSF [Homo sapiens] gi|1572721 38 152195 2 0.9 9.53 Membrane associated guanylate kinase 2 [Homo sapiens] gi|2947232 39 159690 2 1.7 6.04 Membrane interacting protein of RGS16 [Canis familiaris] gi|73978921 43 31984 3 3.3 5.52 Meprin A subunit alpha precursor (-2) gi|2499910 44 85398 4 1.5 5.42 Methylmalonic aciduria type A [Ornithorhynchus anatinus] gi|149637765 45 56480 2 2 9.4 Microsomal glutathione S-transferase 3 isoform 2 [Gallus gallus] gi|50751077 65 15811 5 18.2 9.42 Microtubule-associated protein 4 isoform 2 isoform 2 [Canis familiaris] gi|73985664 44 110291 1 1.1 9.27 Mitochondrial aconitase [Homo sapiens] gi|1718502 80 86346 7 10.8 7.14 Mitochondrial Aspartate Aminotransferase gi|443542 685 45188 32 22.2 9.13 homolog 2 [Homo sapiens] gi|7657347 42 33936 2 4.6 8.25 Mitochondrial complex I subunit NDUFA7 [Gallus gallus] gi|50760928 345 12592 11 28.7 10.33 Mitochondrial complex I subunit NDUFS3 isoform 2 [Gallus gallus] gi|118091521 185 29328 11 20.2 6.55 Mitochondrial complex I subunit NDUFS6 [Gallus gallus] gi|50736146 153 14318 6 47.7 9.22 Mitochondrial import receptor Tom22 [Homo sapiens] gi|9910382 40 15512 2 8.5 4.27 Mitochondrial malate dehydrogenase 2, NAD [Balaenoptera physalus] gi|89574147 391 29216 22 28.7 8.39 Mitochondrial ribosomal protein L50 [Canis familiaris] gi|73971893 44 18292 4 8.8 8.86 Mitochondrial trifunctional protein, alpha subunit [Gallus gallus] gi|45384238 160 83818 9 9.7 9.19 Mitofilin [Gallus gallus] gi|57530041 368 79543 28 29.4 5.72 Mitogen-activated protein kinase kinase kinase kinase 4 [Gallus gallus] gi|71895623 45 140676 4 0.6 8.89 Mmitochondrial ATP synthase alpha subunit isoform 1 [Struthio camelus] gi|115334532 1511 16923 68 63.5 5.35 MOB1 [Homo sapiens] gi|38194905 99 10552 10 12.1 9.34 MTG8-related protein ETO-2 [Mus musculus] gi|2723941 46 69070 4 1.3 7.15 Multidrug resistance protein gi|307375 98 21710 7 39.7 5.84 Muscle 3-Phosphoglycerate Kinase gi|13399644 42 43722 2 2.9 8.78 Mutant cysteine-rich FGF receptor [Gallus gallus] gi|1480467 146 126226 6 5.5 6.53 Myelin basic protein [Gallus gallus] gi|45384134 150 18797 15 43.7 11.6 Myelin P0 protein precursor (Myelin protein zero) (Myelin peripheral protein) (MPP)gi|585535 241 27621 28 28.1 9.59 Myosin alkali light chain gi|212395 49 17200 3 14.6 4.63 Myosin heavy chain (MHY11) (5~partial) [Homo sapiens] gi|2104553 98 215017 10 4.3 5.45 Myosin heavy chain nonmuscle gi|212449 305 229866 23 12.5 5.42 Myosin IB [Bos taurus] gi|397403 43 119023 1 1 9.35 Myosin IF [Bos taurus] gi|119894871 41 125542 1 2.2 9.21 Myosin II heavy chain A nonmuscle [Xenopus laevis] gi|148225656 98 227639 8 3.7 5.44 Myosin regulatory light chain, isoform L20-B [Gallus gallus] gi|45384410 89 19956 3 18 4.67 Myosin-VIIa [Gallus gallus] gi|118103678 44 105691 4 1 8.72 Myosin, heavy polypeptide 7, cardiac muscle, beta [Canis familiaris] gi|74002605 40 242801 1 0.4 6.25 Myosin, heavy polypeptide 9, non-muscle [Gallus gallus] gi|45382693 154 227446 17 9 5.47 N-acetyltransferase 1 [Gallus gallus] gi|45382975 41 33122 1 3.5 5.56 Na K ATPase [Gallus gallus] gi|14330322 4483 41910 144 38.4 5.03 Na(+)/H(+) exchanger 2 gi|73970025 51 91269 2 1.4 9.01 Na(+)/K(+) ATPase alpha-1 subunit gi|2493013 6367 114012 201 20.4 5.32 Na+/K+ ATPase transporting alpha 4 [Equus caballus] gi|149755959 1908 111895 69 7.9 5.64 Na+/K+ transporting ATPase, alpha 1 polypeptide [Gallus gallus] gi|45382945 8290 113528 399 45.6 5.5 NADH dehydrogenase (ubiquinone) [Gallus gallus] gi|118090950 369 24379 24 34.4 5.84 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa [Gallus gallus]gi|148224812 200 13440 10 41.4 6.59 NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa [Gallus gallus] gi|57529753 549 80609 32 24.5 6.5 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 [Gallus gallus] gi|118083465 150 18861 7 33.5 9.46 NADH dehydrogenase [ubiquinone] flavoprotein 2 ([Gallus gallus] gi|118086790 225 27218 18 26.9 7.6 NADH:ubiquinone oxidoreductase b17.2 subunit isoform 2 [Gallus gallus] gi|50728500 42 21937 1 9 9.7 Nanog [Rattus norvegicus] gi|159132563 41 35553 1 2.6 8.75 Natural killer cell enhancing factor isoform 4 [Gallus gallus] gi|50751518 131 22529 11 32.7 8.24 NCAM1, Neural cell adhesion molecule [Homo sapiens] gi|2190958 44 137652 2 1 5.54 Neuritin 1, partial [Ornithorhynchus anatinus] gi|149471517 43 32447 2 3.3 9.06 Neuronal double zinc finger protein [Monodelphis domestica] gi|126336032 40 431771 1 0.8 6.74 Neuronatin, isoform CRA_c [Rattus norvegicus] gi|149043096 40 13692 1 7 11.38 Nitric oxide synthase [Ornithorhynchus anatinus] gi|149632948 53 132624 6 0.8 8.77 Non-metastatic cells 2, protein (NM23B) expressed in [Gallus gallus] gi|45384260 66 17448 7 33.3 7.72 Non-specific lipid-transfer protein (Propanoyl-CoA C-acyltransferase) gi|2501195 40 59452 1 2 8.49 Novel immune-type receptor 12 [Danio rerio] gi|70887597 39 36520 2 3.1 8.36 Novex-3 Titin Isoform [Homo sapiens] gi|17066106 42 634993 2 0.1 5.53 Nuclear mitotic apparatus protein 1,, partial [Danio rerio] gi|125854156 42 218262 1 0.5 5.02 Nuclear protein, NP220 [Homo sapiens] gi|1374698 43 221975 2 0.8 6.01 Nuclear receptor co-repressor 1 [Rattus norvegicus] gi|109488269 44 281841 2 2.1 9.45 Nuclear receptor subfamily 1, group D, member 2 [Macaca mulatta] gi|109052560 41 73244 5 2 8.87 Nucleoside diphosphate kinase [Canis familiaris] gi|73963227 53 17208 2 11.2 5.5 Odd Oz/ten-m homolog 3 [Danio rerio] gi|18859469 40 292568 1 0.8 5.94 Olfactory receptor MOR175-3 [Monodelphis domestica] gi|126333216 48 37570 7 3.4 8.9 Olfactory receptor Olfr314 [Bos taurus] gi|119895337 40 40012 2 3.4 8.75 Olfactory receptor OR19-6 [Bos taurus] gi|119920937 46 45335 2 2 8.21 ORF1 [Ornithorhynchus anatinus] gi|149612445 44 42749 3 2.8 9.32 Otoferlin [Gallus gallus] gi|118089149 41 229785 3 2.1 5.62 Outer mitochondrial membrane cytochrome b5 [Gallus gallus] gi|71895491 220 16204 7 23.6 5 Ovary-specific acidic protein [Gallus gallus] gi|118089893 54 20868 2 13.4 4.13 Oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) [Gallus gallus] gi|71897293 286 116305 25 18.1 6.56 p32 subunit of splicing factor SF2 [Gallus gallus] gi|5509946 159 23783 6 18.4 4.41 PARP9 protein [Gallus gallus] gi|118093859 47 89858 1 1.1 7.03 Parvalbumin [Bos taurus] gi|115497820 40 12074 2 10.9 5.16 Peptidyl arginine deiminase, type III [Gallus gallus] gi|45384274 37 75303 2 5.1 5.76 Peptidylprolyl isomerase B (cyclophilin B) [Gallus gallus] gi|45382027 200 22456 20 29.5 9.4 Peroxiredoxin 1 [Rattus norvegicus] gi|109465923 51 11175 5 18 5.76 Phosphatidylethanolamine-binding protein 1 (PEBP-1) [Gallus gallus] gi|50756703 52 21115 2 17.1 6.96 Phosphatidylinositol 3-kinase delta catalytic subunit gi|2076751 56 123398 5 1 6.87 Phosphatidylinositol-4-phosphate 5-kinase-like 1 [Canis familiaris] gi|73968174 40 79169 1 1.1 9.74 Phosphoglucomutase 2 [Ornithorhynchus anatinus] gi|149642231 43 53119 4 2.4 9.07 Phosphoglycerate kinase 1 [Gallus gallus] gi|45384486 70 45087 5 9.6 8.31 Phospholipid hydroperoxide glutathione peroxidase [Gallus gallus] gi|24080794 48 19555 2 8.2 7.68 Phospholipid-transporting ATPase IF (ATPase class I type 11B) [Bos taurus] gi|119880351 46 136652 1 0.9 6.29 Phosphorylase b kinase regulatory subunit beta (Phosphorylase kinase subunit beta)gi|125532 44 126299 2 0.8 6.95 Pim-2 protooncogene homolog [Pan troglodytes] gi|114688494 45 47274 2 3 6.83 Plasma membrane calcium ATPase 2 isoform 1 [Gallus gallus] gi|118096785 197 138225 5 3.1 5.68 PMCA1bx [Rana catesbeiana] gi|12963455 74 135623 4 3.1 5.74 Polyamine modulated factor 1 binding protein 1 [Mus musculus] gi|9910570 52 120467 2 1 6.17 Polymerase (RNA) III (DNA directed) polypeptide H [Gallus gallus] gi|118082710 48 23459 4 5.8 4.41 Potassium voltage-gated channel, KQT-like subfamily, member 4 [Homo sapiens]gi|119627601 45 11153 1 37.1 8.31 Potassium voltage-gated channel, subfamily Q, member 1 [Gallus gallus] gi|118091304 57 72899 1 4 9.67 Ppar Gamma Cocrystal gi|5107774 83 30833 5 3.7 5.76 Prdx3 protein [Gallus gallus] gi|118093103 432 31428 27 19.6 8.4 Procollagen alpha 1 type II [Gallus gallus] gi|31340542 97 120499 4 2.1 7.22 Progesterone receptor membrane component 2 [Gallus gallus] gi|57530130 57 21685 2 15.9 5.26 Prohibitin isoform 2 [Gallus gallus] gi|50760715 660 29935 29 46.3 5.57 Proliferation associated gene (pag) [Ornithorhynchus anatinus] gi|149632365 61 22406 9 25.6 6.96 Prolyl-4-hydroxylase (AA 5 - 494) [Gallus gallus] gi|63739 89 55174 5 9.4 4.66 protein 14-3-3 [Homo sapiens] gi|5803227 177 28032 12 17.6 4.68 Protein disulfide isomerase family A, member 4 [Gallus gallus] gi|57530768 307 71285 26 30.5 4.96 Protein disulfide isomerase-associated 3 precursor [Gallus gallus] gi|45383890 71 56546 9 9.1 5.76 Protein disulfide isomerase-related protein P5 precursor [Ictalurus punctatus] gi|85719991 72 33742 2 6.2 5.77 Protein disulfide-isomerase A4 precursor (Protein ERp-72) [Macaca mulatta] gi|109069368 74 7835 2 14.7 9.52 Protein kinase C inhibitor protein 1) 14-3-3 protein zeta/delta gi|112696 131 28010 11 22.4 4.77 Protein kinase C-theta gi|558099 42 83522 1 2.8 7.86 Protein kinase, DNA-activated, catalytic polypeptide [Gallus gallus] gi|45382811 43 477303 2 0.2 7.09 Protein SET (Phosphatase 2A inhibitor I2PP2A) (I-2PP2A) [Macaca mulatta] gi|109110116 39 33485 2 2.8 4.23 Protein tyrosine phosphatase, non-receptor type 2 [Xenopus laevis] gi|148231597 39 54747 2 2.6 6.82 Protein tyrosine phosphatase, receptor type, N polypeptide 2 [Rattus norvegicus]gi|13928818 47 112592 3 1.1 5.48 Pyruvate carboxylase [Gallus gallus] gi|45383466 65 128030 3 3.7 6.26 Pyruvate kinase, muscle [Gallus gallus] gi|45382651 204 58434 16 9.8 7.29 Pyruvate kinase, muscle [Ornithorhynchus anatinus] gi|149612407 47 30862 5 8.6 6.09 Rab coupling protein isoform 3 [Rattus norvegicus] gi|109504361 52 97750 2 1 5.67 Rab interacting lysosomal protein-like 1 [Mus musculus] gi|10946796 44 47351 1 1.7 5.09 RAB1, member RAS oncogene family [Macaca mulatta] gi|109100422 38 11904 2 10.6 6.21 RAB10, member RAS oncogene family [Mus musculus] gi|7710086 47 22755 5 11.5 8.59 Rab15 protein [Mus musculus] gi|15489394 63 19558 8 13.1 5.93 RAB18, member RAS oncogene family [Mus musculus] gi|6755258 47 23306 1 9.2 5.24 RAB1A, member RAS oncogene family [Homo sapiens] gi|4758988 244 22891 21 60.5 5.93 RAB26, member RAS oncogene family [Monodelphis domestica] gi|126335536 57 28582 5 9.6 9.58 Rab3 GTPase-activating protein catalytic subunit, (Rab3-GAP p130) (Rab3-GAP) gi|62510941 41 87558 1 1.3 5.56 RAB33B, member of RAS oncogene family [Mus musculus] gi|8394133 57 26206 4 4.8 7.62 RAB35, member RAS oncogene family [Homo sapiens] gi|5803135 63 23296 8 10.9 8.52 RAB3C, member RAS oncogene family isoform 2 [Mus musculus] gi|149264762 45 25362 2 5.9 4.98 RAB5C, member RAS oncogene family [Gallus gallus] gi|45383121 54 23767 2 12 8.64 RAB6A, member RAS oncogene family [Danio rerio] gi|47550805 57 20448 5 13.8 6.4 Rab7 [Mus musculus] gi|1050551 85 23829 2 6.8 7.53 Ral guanine nucleotide dissociation stimulator [Equus caballus] gi|149758418 39 59521 2 1.9 6.16 Ran GTPase-activating protein 1 [Canis familiaris] gi|73969443 38 143903 2 0.8 5.46 Ranbp3 [Monodelphis domestica] gi|126323266 42 67305 2 1.6 5.11 Rap1-interacting adaptor molecule [Ornithorhynchus anatinus] gi|149634720 42 93916 1 1.1 8.19 Ras-related protein O-Krev precursor gi|131854 404 21260 15 13.6 5.69 Ras-related protein RAP1 [Oikopleura dioica] gi|47933428 36 23589 3 5.3 8.59 Recombination activating gene 1 [Heloderma suspectum] gi|56422939 47 109433 2 1.4 8.92 Relaxin 3 receptor 1 [Rattus norvegicus] gi|56605940 39 52794 4 4.4 8.86 Respiratory Complex Ii With Oxaloacetate And Ubiquinone gi|85544000 178 69098 16 32.5 6.17 Retinoic acid early transcript 1L [Rattus norvegicus] gi|61556838 41 37169 2 3.4 6.46 Retinoid x receptor interacting protein [Canis familiaris] gi|73954002 44 99414 5 1.5 6.26 Ribosomal protein 16S gi|200796 81 16460 4 7.6 10.21 Ribosomal protein 60S L24 [Gillichthys mirabilis] gi|10121631 48 17813 2 8.3 11.46 Ribosomal protein L18 [Gallus gallus] gi|44968046 47 18895 3 24.7 11.84 Ribosomal protein L22 [Mus musculus] gi|149248848 42 34834 2 8.6 11.39 Ribosomal protein P1 isoform 1 [Homo sapiens] gi|4506669 108 11621 9 14 4.26 Ribosomal protein S13 [Homo sapiens] gi|4506685 86 17212 7 32.5 10.53 Ribosomal protein S14 [Mus musculus] gi|3097244 71 16462 4 7.3 10.14 Ribosomal protein S18 [Pagrus major] gi|37779106 44 16230 5 14.3 11.11 Ribosomal protein S27a [Mus musculus] gi|94400086 50 15111 3 9.8 9.43 Ribosomal protein S28 [Homo sapiens] gi|4506715 38 7893 2 33.3 10.7 Ribosomal protein S3A [Gallus gallus] gi|129270064 68 30076 5 18.6 9.74 Ribosomal protein S4, X-linked X isoform variant [Pan troglodytes] gi|114680775 80 14793 5 9.4 9.54 Ribosomal protein S5 gi|550021 214 22934 13 23.5 9.59 RNA binding motif protein 15B [Rattus norvegicus] gi|109483938 59 96223 2 1.5 9.85 RNA polymerase II transcription factor SIII subunit A2 [Macaca mulatta] gi|109149521 41 5286 2 17.3 7.93 Roundabout-like protein 4 [Danio rerio] gi|33331379 46 126013 5 0.9 6.97 Rreplication factor C large subunit [Anas platyrhynchos] gi|1399917 45 128406 2 1.2 9.35 Rs13 protein [Ciona intestinalis] gi|74096049 47 17085 3 15.9 10.49 Rtdr1-prov protein [Gallus gallus] gi|50756627 42 37811 2 2.1 6.47 Runt-related transcription factor [Danio rerio] gi|154090991 45 66180 4 3.9 7.66 S-phase kinase-associated protein 2 isoform 1 [Canis familiaris] gi|73954319 42 82595 2 1.7 9.97 Saccharopine dehydrogenase (putative) [Gallus gallus] gi|61097999 315 47224 36 38.9 9.13 Saxitoxin and tetrodotoxin-binding protein 2 precursor gi|27734588 41 44599 3 2.3 5.05 SDHALP2 protein [Homo sapiens] gi|116283954 52 17170 2 8.1 6.14 Sec1 family domain containing 2 [Monodelphis domestica] gi|126331741 40 76011 1 2.2 6.59 Serine/threonine kinase PSKH2 [Equus caballus] gi|149721405 43 59057 3 1.7 9.94 SH3 domain binding glutamic acid-rich protein like [Homo sapiens] gi|4506925 41 12766 1 10.5 5.22 Sialic acid binding Ig-like lectin 15 [Mus musculus] gi|155372047 40 37464 2 2 8.56 Sodium channel associated protein 2 [Monodelphis domestica] gi|126321216 46 103361 1 1.1 6.1 Soluble liver antigen/liver pancreas antigen (Homo sapiens) gi|126341258 38 135532 2 0.9 6.43 Solute carrier family 12 member 2 (Basolateral Na-K-Cl symporter) gi|1709293 225 131666 16 5.1 6.8 Solute carrier family 25 member 3 [Gallus gallus] gi|57525378 393 37910 28 23.3 9.33 Solute carrier family 25 member 12 [Gallus gallus] gi|118093633 131 70995 6 6.5 8.62 Solute carrier family 25 member 5 gi|113459 1790 33102 78 27.2 9.76 Solute carrier family 25 member 6 [Gallus gallus] gi|54020693 1890 32955 93 43 9.73 Solute carrier family 25, member 13 (citrin) [Gallus gallus] gi|61098440 256 74455 14 19.3 8.93 Sorcin [Gallus gallus] gi|124249424 82 22208 2 16.2 5.37 Spastic ataxia of Charlevoix-Saguenay (sacsin) [Gallus gallus] gi|118085040 45 520144 3 0.6 6.23 Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) [Gallus gallus] gi|110227609 5518 285986 238 44.9 5.21 Spectrin, beta, non-erythrocytic 1 [Gallus gallus] gi|118087525 1566 274739 102 29.5 5.37 Spir-2 protein [Mus musculus] gi|27151755 50 81470 5 1.3 7.19 Splicing factor, arginine/serine-rich 8 [Bos taurus] gi|119909121 42 104539 2 1.5 7.88 Strumpellin [Ornithorhynchus anatinus] gi|149410138 40 134406 2 0.9 7.02 Succinate dehydrogenase [ubiquinone] flavoprotein subunit [Canis familiaris] gi|74003064 153 74087 10 16.8 7.29 Sulfhydryl oxidase [Monodelphis domestica] gi|126306477 44 95877 2 1.1 6.87 Surface 4 integral membrane protein [Homo sapiens] gi|2414516 121 28724 2 5.1 8.36 SWI/SNF chromatin remodeling complex subunit OSA2 [Homo sapiens] gi|22597106 37 230824 2 2.9 6.23 Synaptotagmin [Halocynthia roretzi] gi|11559313 39 41207 1 2.2 8.75 t-SNARE domain containing 1 [Homo sapiens] gi|21450719 41 56532 1 1.9 9.17 Talpid3 [Gallus gallus] gi|104294880 42 166830 2 0.7 5.33 TBC1 domain family, member 21 [Canis familiaris] gi|74000971 41 38760 4 2.1 5.72 TBP-associated factor 11 [Homo sapiens] gi|5032151 41 23350 2 4.7 4.78 Tensin 4 [Bos taurus] gi|84000287 41 70874 3 1.8 6.97 Testis expressed protein 14 [Gallus gallus] gi|118100294 67 119332 7 1.4 5.55 Thioredoxin [Gallus gallus] gi|45382053 48 11978 2 12.4 5.1 Thyroid adenoma associated [Gallus gallus] gi|158519797 39 219438 2 0.5 6.07 Titin [Homo sapiens] gi|1212992 40 3011888 2 0.1 6.35 Transducin beta chain 1) gi|3023838 89 38161 7 17.9 5.6 Transferrin receptor [Monodelphis domestica] gi|126325789 47 86058 3 1.4 5.54 Transmembrane cochlear-expressed protein 2 [Canis familiaris] gi|73991996 41 102459 1 1 9.62 Transmembrane emp24 domain-containing protein 10 [Gallus gallus] gi|57529934 155 25016 8 20.1 6.37 Transmembrane protein 132C [Equus caballus] gi|149720797 37 137531 3 1 8.56 Treacher Collins-Franceschetti syndrome 1 [Bos taurus] gi|119895727 50 149554 2 0.6 9.12 Triose Phosphate Isomerase From Chicken Muscle gi|230359 127 26755 7 22.3 7.26 Troponin C-like protein gi|223036 91 16696 2 10.8 4.12 TUBB [Salmo salar] gi|126417160 52 16812 3 20.6 4.82 Tubulin 3 alpha [Ciona intestinalis] gi|21667231 61 44564 2 3.5 5.85 Tubulin 5-beta [Homo sapiens] gi|35959 52 50055 3 7.2 4.81 Tubulin alpha [Homo sapiens] gi|32015 55 50503 3 3.1 4.95 U1 small nuclear ribonucleoprotein 1C [Ornithorhynchus anatinus] gi|149412853 42 126964 2 1.3 8.83 Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 [Gallus gallus]gi|57524866 157 29710 6 20.6 8.68 UDP-glucose ceramide glucosyltransferase-like 2 [Monodelphis domestica] gi|126337535 45 175679 3 0.5 7.19 Unknown (protein for MGC:184828) [Xenopus tropicalis] gi|170284510 5773 114213 188 22.6 5.26 Upregulated during skeletal muscle growth 5 [Homo sapiens] gi|14249376 61 6510 5 17.2 9.78 Ureidopropionase, beta [Danio rerio] gi|169158994 41 32570 2 4.3 9.24 Vacuolar protein sorting 13D isoform 1 [Canis familiaris] gi|73965437 41 170390 1 0.8 5.65 Valosin-containing protein [Gallus gallus] gi|113206112 92 89953 12 13.9 5.14 Vertebrate differentially expressed in FDCP 6 homolog (mouse) (DEF6) [Danio rerio]gi|94733528 40 68922 2 2.9 5.54 Vertebrate IQ motif containing GTPase activating protein 2 (IQGAP2) [Danio rerio]gi|122891262 38 192430 1 0.8 6.11 Vesicle amine transport protein 1 homolog (T californica) [Gallus gallus] gi|118103033 57 41993 2 2.9 6.18 Villin 1 [Gallus gallus] gi|118085502 42 97854 2 3.6 5.77 VIP17/MAL proteolipid [Ornithorhynchus anatinus] gi|149636595 53 32779 3 3.3 8.98 Voltage gated potassium channel [Homo sapiens] gi|2465515 52 65590 1 4.5 9.72 Voltage-dependent anion channel 1 [Gallus gallus] gi|76443696 356 30744 25 29.3 6.85 Voltage-dependent anion-selective channel protein 2 (VDAC-2) gi|11134020 3993 30162 166 58.5 8.63 Vomeronasal receptor V1RF3 isoform 1 [Equus caballus] gi|149738010 3844 285441 164 32 5.22 Von Willebrand Factor [Echimys chrysurus] gi|12053747 41 47183 2 3.1 6.13 Xylulokinase homolog [Homo sapiens] gi|18860918 46 59086 3 2.4 5.55 Zinc finger and SCAN domain containing 4 [Rattus norvegicus] gi|62651948 42 58505 4 2.2 6.55 Zinc finger protein 157 (HZF22) [Canis familiaris] gi|74007352 41 59795 3 1.6 9.03 Zinc finger protein 592 [Mus musculus] gi|30520115 43 135333 7 0.8 8.6 Zinc finger protein 598 [Monodelphis domestica] gi|126335524 56 102935 5 1.4 9.27 Zinc finger, CDGSH-type domain 1 [Gallus gallus] gi|118092479 117 12141 6 36.1 8.84