Supporting Information for Proteomics DOI 10.1002/pmic.200500516

Maarit S. Takatalo, Petri Kouvonen, Garry Corthals, Tuula A. Nyman and Ragna H. Rnnholm

Identification of new Golgi complex specific proteins by direct organelle proteomic analysis

ª 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Supplementary Table 1. Identified proteins from rat liver Golgi sample. Proteins identified with protein score above 1.3 with ProID, or peptide scores above 32/41 with Mascot grouped based on their classification. Protein classification is based on the cellular localization or the protein function data in the Swiss-Prot entry. Proteins are listed in the table in alphabetical order.

Name of the Protein Accession number Identification Distinct Peptides Score Mascot ProID Mascot ProID Unused ProtSc Exp.1 Exp.2 Exp.1 Exp.2 Exp.1 Exp.2 Exp.1 Exp.2

SW NCBI SW SW SW SW SW SW SW SW NCBI NCBI NCBI NCBI NCBI NCBI NCBI NCBI Golgi complex 1 27 kDa Golgi SNARE protein O35165 gi|12643479 3 4 4 5 76 67 3.40 2.85 228 kDa Golgi SNARE protein Q62931gi|111319634443 437668137120 4.593.38 45 kDa calcium-binding protein 3 Q91ZS3gi|21263446546532871071001551552.012.007.547.35 [Precursor] 4-hydroxyphenylpyruvate dioxygenase 4 P32755 gi|417146 2 1 5 4 47 47 2.02 2.01 [Fragment] Adapter-related protein complex 1 beta 5 P52303 gi|1703168 8 8 12 10 227 214 11.71 9.50 1 subunit Adapter-related protein complex 4 Q9WVL1 6 gi|13431286 2 35 sigma 1 subunit mouse Adaptor-related protein complex 1, mu Q9WVP1 7 gi|13123951 4 3 75 67 2 subunit mouse 8 ADP-ribosylation factor-like protein 1 P61212 gi|47117641 2 5 3 2 82 79 3.40 3.30 Aflatoxin B1 aldehyde reductase 9 Q8CG45 gi|39930812 5 2 2.00 2.00 member 2 Q99996 10 A-kinase anchor protein 9 gi|14194461 3 17 4 61 2.82 1.53 human 11 Alpha 2,8-sialyltransferase P70554 gi|81870571 6 4 4 3 45 45 2.01 4.00 Alpha-1,3-mannosyl-glycoprotein 2- 12 Q09325 gi|1169977 12 11 11 10 11 9 8 8 311 269 287 279 11.42 9.16 13.21 12.91 beta-N-acetylglucosaminyltransferase Alpha-1,6-mannosyl-glycoprotein 2- 13 Q09326gi|1169978655455641911812101997.536.036.006.00 beta-N-acetylglucosaminyltransferase Alpha-1,6-mannosylglycoprotein 6- 14 beta-N-acetylglucosaminyltransferase Q08834 gi|729609 3 2 5 2 61 61 2.00 2.00 V Alpha-2,6-sialyltransferase 15 Q6ZXY0 gi|46425428 1 2.00 ST6GalNAc VI [Fragment] 16 Alpha-6-fucosyltransferase Q6EV76 gi|50057053 3 4 4 5 78 125 3.24 5.31 17 Alpha-mannosidase II [Fragment] P28494 gi|126723 26 25 29 29 24 21 37 32 853 623 1366 1240 22.73 19.16 32.97 43.89 18 ARF-related protein Q63055 gi|2492928 2 2 1 1 94 87 2.00 2.00 Q91Z92 19 Beta-1,3-galactosyltransferase 6 gi|61211862 2 5 3 64 2.00 2.56 mouse Beta-1,4 N- 20 Q10468 gi|51858903 4 4 5 4 113 96 4.16 3.42 acetylgalactosaminyltransferase Calcium-transporting ATPase type 2C 21 Q64566 gi|202864 7 5 10 9 5 5 11 8 54 54 317 299 1.53 1.37 12.30 12.09 member 1 CMP-N-acetylneuraminate-beta-1,4- 22 Q02734 gi|12850118 5 3 7 6 61 58 4.05 3.74 galactoside alpha-2,3-sialyltransferase CMP-N-acetylneuraminate-beta- 23 galactosamide-alpha-2,3- P61131 gi|47116964 6 35 sialyltransferase CMP-N-acetylneuraminate-beta- 24 galactosamide-alpha-2,6- P13721 gi|115446 9 8 10 10 7 7 11 10 509 429 713 688 11.52 10.33 15.26 15.56 sialyltransferase Conserved oligomeric Golgi complex Q9Z160 25 gi|22653703 8 7 8 33 2.01 2.01 component 1 mouse Conserved oligomeric Golgi complex Q921L5 26 gi|25453261 2 2 3 41 41 2.00 component 2 mouse 27 Copper-transporting ATPase 2 Q64535 gi|312172 4 13 6 67 3.13 2.61 P59103 28 D-amino acid oxidase activator gi|25452964 1 39 human Q9EPS3 29 D-glucuronyl C5-epimerase gi|25090478 5 6 7 6 68 63 3.46 3.32 mouse 30 DMT1-associated protein Q5XI18 gi|54035576 5 8 10 117 3.24 17.71 31 Fatty-acid amide hydrolase P97612 gi|6225312 4 3 55 52 Formimidoyltransferase- 32 O88618 gi|21431757 7 12 9 8 298 286 13.27 12.45 cyclodeaminase 33 Furin [Precursor] P23377 gi|56172 5 3 4 2 110 103 2.01 2.00 Galactosylgalactosylxylosylprotein 3- P58158 34 gi|14285358 5 4 7 42 117 6.01 beta-glucuronosyltransferase 3 mouse 35 GD3 alpha 2,8-sialyltransferase P97877 gi|1903381 3 3 4 3 81 77 4.00 4.00 36 General vesicular transport factor p115 P41542 gi|1171952 13 12 15 16 10 11 14 13 367 309 678 632 10.07 9.46 24.96 23.05 37 Gnptag_predicted protein [Fragment] Q4G066 gi|71051699 1 43 38 Golgi apparatus protein 1 [Precursor] Q62638 gi|17376577 25 22 23 20 23 20 22 19 389 290 545 480 14.43 12.12 24.96 24.98 Golgi autoantigen, golgin subfamily A 39 Q62839 gi|6226622 21 21 27 24 19 18 26 25 614 523 1301 1228 12.87 11.16 39.37 39.38 member 2 Golgi autoantigen, golgin subfamily A P55937 40 gi|81175171 18 6 15 217 124 10.31 member 3 mouse 41Golgi phosphoprotein 3 Q9ERE4gi|504002153243 357165122118 4.004.00 42Golgi reassembly stacking protein 1O35254gi|513156892222222357571051002.002.004.004.00 43 Golgi reassembly stacking protein 2 Q9R064 gi|51315736 1 3 3 4 103 105 4.00 5.39 44 Golgi resident protein GCP60 Q7TNY6 gi|33469059 8 8 11 11 7 34 9 54 104 127 323 335 3.57 18.29 16.00 84.05 45 Golgin-84 Q3ZU82 gi|37720821 14 15 17 22 11 11 19 23 329 351 552 899 10.59 12.21 24.29 42.14 GRIP and coiled-coil domain- Q8CHG3 46 gi|32469711 9 36 containing protein 2 mouse Heparan sulfate N-deacetylase/N- 47 Q02353 gi|401136 3 10 10 12 11 37 298 268 15.74 15.26 sulfotransferase Q80TN5 48 Huntingtin-interacting protein 14 gi|46395762 3 3 5 74 74 2.01 mouse 49 Hypothetical protein Q497A2 gi|71680968 1 1.70 50 LOC361315 protein Q5XID0 gi|53733545 1 2.00 51 mannosidase 1, alpha - gi|75905483 5 10 10 15 5 7 11 14 232 405 604 769 5.04 5.17 18.56 21.38 Membrane-bound transcription factor 52 Q9WTZ3 gi|17367438 4 3 7 6 46 46 2.02 2.01 site-1 protease [Precursor] Mid-1-related chloride channel 2; Mid- Q8VIF1 gi|17736804 53 1-related chloride channel 1; Q9WU61 gi|14278955 243 LOC170927 protein Q66HQ5 gi|51858922 N-deacetylase/N-sulfotransferase 54 - gi|62661015 3 2 58 2.00 (heparan glucosaminyl) 2 (predicted) Neutral alpha-glucosidase AB Q8BHN3 55 gi|2104689 5 6 6 4 7 78 131 124 3.05 4.69 [Precursor] mouse 56 NSFL1 cofactor p47 O35987 gi|41017427 2 2 2 53 53 1.40 57 Nucleobindin 1 [Precursor] Q63083 gi|2493471 22 20 31 30 19 18 30 30 710 552 1390 1285 20.20 17.58 54.35 54.32 58 Nucleobindin 2 [Precursor] Q9JI85 gi|14549433 12 12 20 18 10 9 14 15 458 396 1070 874 12.64 12.68 24.40 23.61 59 Phosphatidylinositol 4-kinase beta O08561 gi|38372399 4 41 Phosphatidylinositol-binding clathrin 60 O55012 gi|44888251 3 2 2 73 2.00 2.00 assembly protein Polypeptide N- 61 Q10473gi|1709559337733131089741441664.003.4014.0411.31 acetylgalactosaminyltransferase 1 Polypeptide N- 62 Q6P6V1 gi|38303875 4 4 6 5 88 78 2.96 2.49 acetylgalactosaminyltransferase 11 63 Polysialyltransferase [Fragment] O08563 gi|81870371 4 2.01 64 Prenylated Rab acceptor protein 1 O35394 gi|55562836 3 3 3 3 176 163 6.00 6.00 65Protein-tyrosine sulfotransferase 2 Q5RJS8gi|557786997455318569611721352.022.006.125.70 66Ras-related protein Rab-10 P35281gi|464553444453542241853713552.001.704.004.00 67 Ras-related protein Rab-12 [Fragment] P35284 gi|464555 3 2 309 266 68 Ras-related protein Rab-1A Q6NYB7 gi|74185239 12 12 9 9 10 10 12 348 339 587 296 1.82 7.14 6.51 69 Rat GCP360 Q63714 gi|516826 16 48 25 61 19 67 470 150 1775 6.42 70RGD1306324_predicted protein Q498C8gi|716812831144 57539289 Q6NZC7 71 SEC23-interacting protein gi|55583895 3 40 mouse 72 Sialyltransferase 10 Q569D2 gi|62205044 3 3 3 179 2.53 6.00 73 Sialyltransferase ST3Gal-I Q6H8N0 gi|49203091 5 6 7 4 7 7 60 205 275 2.56 10.00 11.30 74 similar to alpha-mannosidase - gi|62644086 9 21 19 6 4 18 16 243 744 672 4.70 3.32 23.95 25.05 75 similar to B3gnt1 protein - gi|27698122 3 2 5 3 45 50 2.03 2.00 similar to beta-1,3-N- 76 - gi|34861816 5 5 5 3 138 127 4.02 5.70 acetylglucosaminyltransferase bGnT-6 similar to carbohydrate (chondroitin 4) 77 - gi|62647791 1 2.00 sulfotransferase 13 similar to component of oligomeric 78 - gi|62650575 3 1.40 golgi complex 5 isoform 1 similar to ectonucleoside triphosphate 79 - gi|62661681 3 2 4 3 82 120 2.00 4.00 diphosphohydrolase 4 similar to golgi autoantigen golgin 80 - gi|62654467 20 22 23 18 123 348 6.16 15.85 subtype a4; tGolgin-1 similar to Golgi autoantigen, golgin 81 - gi|62645049 1 65 subfamily a, 1 82 similar to golgi phosphoprotein 4 - gi|62643583 10 17 6 12 164 473 5.30 13.85 similar to Golgi-specific brefeldin A- 83 - gi|62642410 8 9 11 9 136 164 7.11 8.95 resistance factor 1 similar to heparan sulfate 2- 84 - gi|62644508 4 5 4 4 91 82 5.40 4.16 sulfotransferase 85 similar to male-enhanced antigen-2 - gi|62659085 14 15 315 14.11 86 similar to mKIAA1402 protein - gi|62646643 3 2 77 2.55 similar to RIKEN cDNA 5730410E15 87 - gi|62652375 5 1.41 gene similar to UDP-Gal:betaGlcNAc 88 - gi|348548662321424312311461611.951.783.403.70 beta1,3-galactosyltransferase 1 similar to UDP-N-acetyl-alpha-D- 89 galactosamine:polypeptide N- - gi|62665443 8 6 12 13 5 6 16 15 111 82 485 476 4.12 3.92 23.22 22.24 acetylgalactosaminyltransferase 2 90 similar to vesicle associated membrane - gi|62659601 2 2 3 3 135 138 4.00 4.00 protein 4 similar to Vesicular integral-membrane 91 protein VIP36 precursor (Lectin, - gi|27682691 11 12 7 8 10 11 10 9 259 297 283 278 9.27 10.23 16.00 18.00 mannose-binding 2) Soluble calcium-activated nucleotidase 92 Q8K4Y7 gi|71153846 7 6 15 13 4 3 16 13 99 75 602 542 3.14 2.70 25.42 24.70 1 Sterol regulatory element binding 93 P56720 gi|17380503 5 4 3 40 2.01 2.00 protein 1 [Fragment] 94 Syntaxin-6 Q63635 gi|51858907 3 2 2 2 75 75 2.00 2.00 Q15643 95 Thyroid receptor-interacting protein 11 gi|33302627 8 15 10 37 76 2.01 human 96 Tpst1_predicted protein Q3KR92 gi|76779364 5 7 10 11 6 6 12 87 100 314 308 4.28 5.37 14.12 Trans golgi network (TGN) specific 97 integral membrane protein TGN38 Q63575 gi|57351 5 3 164 4.00 [Precursor] Trans-Golgi network integral 98 P19814 gi|135698 1 5 2 3 39 161 1.31 4.00 membrane protein TGN38 [Precursor] Transitional endoplasmic reticulum 99 P46462 gi|38014694 9 12 20 20 7 5 22 19 116 90 493 459 4.40 3.82 28.87 26.64 ATPase Transmembrane emp24 domain 100 Q63584 gi|1360136 10 10 12 12 10 10 11 11 1036 885 1507 1281 18.00 17.70 20.00 19.31 containing protein 10 [Precursor] Q811I5 101 Trip11 protein [Fragment] gi|28279992 5 89 mouse Type 2 lactosamine alpha-2,3- 102 P61943gi|4240645033634 3 180144166833.01 4.00 sialyltransferase 103 Tyrosylprotein sulfotransferase 1 Q6AYS9 gi|50926141 11 9 309 15.39 UDP-N-acetyl-alpha-D- 104 galactosamine:polypeptide N- Q3KR95 gi|76780269 2 50 acetylgalactosaminyltransferase 4 105 UDP-N-acetylglucosamine transporter Q6AXR5 gi|59798524 1 2 2 2 43 81 2.00 4.00 106 Unknown (protein for MGC:125095) - gi|79152372 5 4 5 3 75 67 2.86 2.98 Vacuolar protein sorting-associated 107 O08700 gi|23396892 4 6 9 6 39 38 1.98 1.54 protein 45 108 Xylosyltransferase 2 Q9EPI0 gi|71164811 4 5 7 5 211 200 6.12 6.04

Transport Adapter-related protein complex 1 beta 1 P52303 gi|1703168 8 8 12 10 227 214 11.71 9.50 1 subunit Adapter-related protein complex 2 2 P18484 gi|113337 7 9 5 73 4.74 4.01 alpha 2 subunit Adapter-related protein complex 2 beta 3 P62944 gi|51702208 7 10 7 124 2.12 1.70 1 subunit 4 ADP-ribosylation factor 5 P84083 gi|56388751 2 2 1 1 42 42 1.30 1.30 5 Alpha-soluble NSF attachment protein P54921 gi|38648848 4 5 10 11 4 3 11 10 63 59 361 339 1.44 1.39 15.68 15.79 P28663 6 Beta-soluble NSF attachment protein gi|47117840 4 84 mouse 7 CDC42 protein Q8CFN2 gi|24637541 2 4 83 2.48 Q8BXK8 8 Centaurin-gamma 2 gi|51315986 7 36 mouse 9 Clathrin coat assembly protein AP50 P84092 gi|51316971 3 4 4 2 54 54 2.00 2.00 10 Clathrin heavy chain P11442 gi|116514 14 13 27 25 10 10 28 24 236 173 713 664 6.64 5.11 43.51 40.72 P53675 11 Clathrin heavy chain 2 gi|2506298 10 156 human 12 Coatomer beta subunit P23514 gi|38197648 8 7 15 8 118 129 6.05 5.35 13 Coatomer delta subunit Q66H80 gi|51858705 7 8 7 8 144 129 10.96 10.58 Coatomer protein complex, subunit 14 Q5M7X1 gi|56789724 5 4 8 5 98 90 4.29 4.11 beta 2 Coatomer protein complex, subunit 15 Q4AEF8 gi|71891599 6 6 10 74 77 1.80 gamma Cop-coated vesicle membrane protein 16 Q63524gi|3914232654465423403111271308.967.084.594.24 p24 [Precursor] 17 Dynein light chain 2, cytoplasmic Q78P75 gi|56748619 2 2 2 2 118 112 4.00 3.70 18 Ehd1_predicted protein Q641Z6 gi|51980417 4 4 2 54 2.00 1.31 19 GTP-binding protein rab14 - gi|420272 3 5 102 449 20 Hypothetical protein Q3B7V5 gi|77567746 5 5 167 162 21 Hypothetical protein LOC500282 Q66HA6 gi|51858691 1 2.00 22 N-ethylmaleimide sensitive factor Q9QUL6 gi|6007811 14 10 18 16 9 7 18 17 158 138 389 365 3.93 3.25 20.27 17.15 23 PRA1 family protein 3 Q9ES40 gi|38494360 2 1 1 1 48 48 1.30 1.70 24 Rab GDP dissociation inhibitor beta-2 P50399 gi|1707891 6 38 25RAB18, member RAS oncogene familyQ5EB77gi|819095603154 757272129105 7.416.15 26 RAB21, member RAS oncogene family Q6AXT5 gi|50927400 4 3 3 3 72 72 2.01 2.00 27Ras-related protein Rab-10 P35281gi|464553444453542241853713552.001.704.004.00 P62494, gi|50402540 28 Ras-related protein Rab-11A, Rab-11B 23123243665872724.004.003.403.70 O35509 gi|50403673 29 Ras-related protein Rab-12 [Fragment] P35284 gi|464555 3 2 309 266 30 Ras-related protein Rab-13 P35286 gi|46577668 2 2 91 83 31 Ras-related protein Rab-14 P61107 gi|46577632 3 5 7 6 110 511 8.00 8.00 32 Ras-related protein Rab-15 P35289 gi|464561 4 2 371 308 33 Ras-related protein Rab-1A Q6NYB7 gi|74185239 12 12 9 9 10 10 12 348 339 587 296 1.82 7.14 6.51 34 Ras-related protein Rab-1B P10536 gi|54673780 12 12 11 11 9 9 15 10 462 427 623 628 7.59 3.00 18.64 19.17 P35285 35 Ras-related protein Rab-22A gi|46577691 2 2 47 47 mouse 36 Ras-related protein Rab-26 P51156 gi|76363526 2 3 309 266 37Ras-related protein Rab-2A P05712gi|131789567656661381283423094.343.7411.4010.89 38 Ras-related protein Rab-31 Q6GQP4 gi|62900806 2 2 3 1 47 47 2.00 2.00 39 Ras-related protein Rab-35 Q5U316 gi|62900797 4 4 371 308 Q8BHC1 40 Ras-related protein Rab-39B gi|74141396 3 3 309 266 mouse 41 Ras-related protein Rab-3A P63012 gi|57008 2 2 309 266 42Ras-related protein Rab-3C P62824gi|13732143222 6969309266 43 Ras-related protein RAB43 Q53B90 gi|50898338 2 266 44 Ras-related protein Rab-4A P05714 gi|131793 2 2 309 266 45 Ras-related protein Rab-4B P51146 gi|1710026 2 309 P35279 46 Ras-related protein Rab-6A gi|13638404 12 10 1 12 11 12 11 285 569 44 10.72 9.47 13.52 13.55 mouse Q9H0N0 47 Ras-related protein Rab-6C gi|27734458 4 3 3 4 54 107 1.30 2.00 human 48Ras-related protein Rab-7 P09527gi|47938948545533451451191701543.951.818.007.70 49 Ras-related protein Rab-8A P35280 gi|49522647 3 3 8 4 386 323 2.00 2.00 50 SAR1a gene homolog 1 Q6AY18 gi|50925795 1 2 3 69 1.40 1.31 51 SAR1a gene homolog 2 Q5HZY2 gi|57032799 5 66 Sec1 family domain containing protein 52 Q62991 gi|51316554 4 5 14 14 5 5 14 13 73 57 640 609 2.59 1.57 22.92 22.19 1 53 Sec22 homolog Q642F4 gi|51980493 2 2 2 65 54 1.70 SEC22 vesicle trafficking protein-like 54 Q4KM74gi|68534274447733772181742772682.662.2511.5210.85 1 55 SEC23A (S. cerevisiae) (predicted) - gi|34867969 10 13 13 9 7 15 16 145 516 505 4.50 2.77 24.09 24.73 Q8CGF4 56 SEC24 related gene family, member C gi|25955503 7 6 10 10 4 4 11 9 65 60 235 324 2.49 2.78 9.49 14.31 mouse secretory carrier membrane protein 3 57 - gi|3485796233453244100941952542.282.096.008.00 (predicted) Secretory carrier-associated membrane 58 P56603 gi|3914958 1 1 3 1 95 95 2.00 2.00 protein 1 Secretory carrier-associated membrane 59 Q9ET20 gi|47116975 1 1 2.00 2.00 protein 4 60 similar to ARL6IP2 - gi|62650248 3 3 68 3.31 similar to Coatomer protein complex 61 - gi|62659750 10 9 10 9 155 180 9.83 11.32 subunit alpha 62 similar to gamma2-adaptin - gi|34874144 3 3 63 2.22 similar to Gamma-soluble NSF attachment protein (SNAP-gamma) (N- 63 - gi|62664521 562356 49571.401.313.412.82 ethylmaleimide-sensitive factor attachment protein, gamma) 64Similar to gp25L2 protein Q5I0E7gi|569704658799779104644026276097.667.4515.9914.10 65 similar to GTPase Rab37 - gi|62657322 4 4 309 266 66 similar to hypothetical protein - gi|62650688 3 2 50 50 67 similar to mBLVR - gi|34862288 8 1.41 similar to nonclathrin coat protein 68 - gi|62662439 1 2 4 2 37 117 3.71 3.70 epsilon-COP similar to Protein transport protein 69 - gi|62645966 10 8 4 133 135 131 Sec23B (SEC23-related protein B) similar to Protein transport protein 70 - gi|27714473 1 2 1 83 2.00 2.00 SEC61 beta subunit similar to RAB, member of RAS 71 - gi|62657933 2 50 oncogene family-like 3 72similar to Rab33B - gi|348573035565 787063367306 6.024.57 similar to RAB39, member RAS 73 - gi|62653964 2 3 309 266 oncogene family 74 similar to RAB5B protein - gi|34862219 5 3 2 4 3 123 115 1.70 6.00 2.00 75 similar to Rab5c protein - gi|27689505 3 4 4 2 3 4 40 153 136 1.40 2.00 6.00 similar to RAB6B, member RAS 76 - gi|62654200 13 10 252 523 oncogene family similar to Ras-related protein Rab-33A 77 - gi|62667400 2 2 43 43 (Small GTP-binding protein S10) similar to Ras-related protein Rab-5C 78 - gi|62643230 4 2 33 116 (RAB5L) (L1880) similar to SEC24 related gene family, 79 - gi|62656049 3 2 69 2.46 member A similar to SEC24 related gene family, 80 - gi|626442865554343358531131252.032.114.004.89 member D similar to Vesicle transport through Q9Z2P7 81 interaction with t-SNAREs 1B gi|4104432 3 2 96 4.00 mouse homolog 82 Small GTP-binding protein rab5 O88565 gi|3309068 4 3 4 101 88 2.00 Synaptic vesicle membrane protein 83 Q3MIE4 gi|75516467 4 5 5 6 85 165 6.00 9.70 VAT-1 homolog 84 Synaptophysin-like protein Q66H18 gi|51859315 2 3 60 2.89 85 Syntaxin 13 O70319 gi|3184552 1 2 1 3 53 76 2.00 3.70 86 Syntaxin-8 Q9Z2Q7 gi|3834382 2 2 5 4 129 122 4.01 3.70 87 TIRAP3b long form Q6JUT2 gi|37677667 7 556 human Vacuolar proton translocating ATPase 88 P25286 gi|206430 7 6 6 5 189 178 6.61 6.49 116 kDa subunit a isoform 1 Vesicle transport through interaction 89 Q9JI51 gi|9719422 5 3 5 4 56 100 5.40 4.16 with t-SNAREs homolog 1A Vesicle transport through interaction O88384 90 gi|13124606 4 4 101 4.02 with t-SNAREs homolog 1B mouse 91 Vesicle-associated membrane protein 3 P63025 gi|51704187 2 2 2 2 59 59 3.40 3.30 92 Vesicle-associated membrane protein 8 Q9WUF4 gi|55976639 1 1 1.40 1.30 Vesicle-associated membrane protein- 93 Q9Z269 gi|24638336 2 2 2 2 57 57 2.26 2.21 associated protein B

ERGIC 1 ERGIC-53 protein [Precursor] Q62902 gi|29611707 9 9 13 13 9 8 14 13 496 434 1132 862 9.23 8.39 20.48 18.93 ER-Golgi intermediate compartment 32 Q9DC16 2 gi|520007333322 2245446565 2.002.00 kDa protein mouse Multiple coagulation factor deficiency 3 Q8K5B3 gi|49036094 1 1 1 2 61 61 2.00 2.00 protein 2 homolog [Precursor] 4Syntaxin-5 Q08851gi|250109322763310881942182172.592.5110.138.69 UDP-glucose:glycoprotein 5 Q9JLA3gi|680529863163 11354545757 2.191.31 glucosyltransferase 1 [Precursor]

ER 1 15 kDa selenoprotein [Precursor] Q923V8 gi|20139870 1 2 1 1 81 81 2.00 2.00 150 kDa oxygen-regulated protein 2 Q63617 gi|10720174 8 8 9 7 195 123 7.18 6.11 [Precursor] 3 beta-hydroxysteroid dehydrogenase 3 P27364 gi|112774 7 6 7 5 145 117 8.01 6.59 type III 3 beta-hydroxysteroid 4 dehydrogenase/delta 5-->4-isomerase Q62878 gi|3334103 3 3 71 71 type IV 78 kDa glucose-regulated protein 5 P06761 gi|121574 13 11 22 21 14 11 27 25 345 304 882 835 10.84 8.08 34.25 32.35 [Precursor] 67-dehydrocholesterol reductase Q9Z2Z8gi|518594084311 3241418383 2.002.00 7Ab1-205 Q7TP91gi|330864782333 5743114110 Alpha-2-macroglobulin receptor- 8 associated protein [Precursor] Q99068 gi|1703291 2 3 2 55 2.00 2.00 [Fragment] 9 Arylacetamide deacetylase Q9QZH8 gi|57012548 3 1 52 52 10 Bile acid CoA ligase Q9ES38 gi|60552090 5 7 149 5.52 11 BWK4 Q5VLR5 gi|37724109 5 8 9 10 4 6 9 10 174 165 285 419 2.70 4.41 9.82 14.38 12 Calnexin [Precursor] P35565 gi|310085 4 5 4 7 4 40 128 134 3.21 2.57 13Calreticulin [Precursor] P18418gi|385659778655446670472332213.752.868.417.94 14 Carboxylesterase [Precursor] O70631 gi|57013350 7 4 174 2.00 15Carboxylesterase 3 [Precursor] P16303gi|568998885879783882201095.033.8111.6710.79 16 Carboxylesterase isoenzyme Q8K3R0 gi|21426807 6 7 158 7.55 17 Carboxylesterase RL1 Q924V9 gi|14331129 5 52 18 Carboxylesterase-like Q68G49 gi|51260613 4 90 19 Carboxylic ester hydrolase Q91YG2 gi|15459757 8 162 Corticosteroid 11-beta-dehydrogenase, 20 P16232 gi|23830928 4 3 3 3 80 76 4.00 4.00 isozyme 1 21 Cytochrome P450 1A2 P04799 gi|117148 1 5 4 4 4 33 174 162 6.00 6.00 22 Cytochrome P450 2A1 P11711 gi|117191 6 6 7 8 166 193 9.53 9.32 23 Cytochrome P450 2A2 P15149 gi|117193 5 5 8 6 197 185 4.00 4.00 24 Cytochrome P450 2A3 P20812 gi|117194 3 3 65 59 25 Cytochrome P450 2B1 P00176 gi|117206 5 3 71 75 26 Cytochrome P450 2B12 P33272 gi|461815 4 3 42 42 27 Cytochrome P450 2B2 P04167 gi|3123191 7 5 71 75 28 Cytochrome P450 2B3 P13107 gi|117210 6 4 3 4 121 119 5.70 5.30 29 Cytochrome P450 2C11 P08683 gi|203695 9 7 13 13 7 6 15 13 144 99 420 425 4.10 4.06 20.69 19.94 30 Cytochrome P450 2C22 P19225 gi|117236 3355436371531151052.002.004.023.73 31 Cytochrome P450 2C23 P24470 gi|6166042 8 7 10 9 7 7 17 13 106 83 307 263 3.49 2.35 18.99 17.49 32 Cytochrome P450 2C6 P05178 gi|117223 3 67329 70 2001782.001.308.00 33 Cytochrome P450 2D1 P10633 gi|117241 86776 126881871731.52 34 Cytochrome P450 2D26 P10634 gi|117242 8 7 14 14 6 6 13 12 101 58 332 295 5.39 4.01 20.57 18.92 35 Cytochrome P450 2D3 P12938 gi|3915646 6488 8710064197183 3.403.30 36 Cytochrome P450 2D4 P13108 gi|2575863 3 3 41 41 37 Cytochrome P450 2D5 P12939 gi|117245 7 7 7 7 250 229 6.00 6.00 38 Cytochrome P450 2E1 P05182 gi|1352193 99886688109942672654.422.7712.2710.73 39 Cytochrome P450 2F4 O35293 gi|3913179 2 1 2.00 2.00 40 Cytochrome P450 3A1 P04800 gi|117153 4 4 3 2 48 44 2.93 1.71 41 Cytochrome P450 3A13 Q5PQX2 gi|56270307 4 36 42 Cytochrome P450 3A2 P05183 gi|6166033 5 36 43 Cytochrome P450 4A1 P08516 gi|117163 2 4 52 52 44 Cytochrome P450 4A2 [Precursor] P20816 gi|51260988 6 6 9 6 208 183 8.12 7.39 45 Cytochrome P450 4A3 [Precursor] P20817 gi|1352184 7531 124902.002.00 46 Cytochrome P450 4F1 P33274 gi|6643935 4 4 4 4 103 89 7.70 7.30 Q9DBW0 47 Cytochrome P450 4V3 gi|71648658 1 5 4 34 2.00 1.31 mouse 48 Cytochrome P450, family 2, subfamily Q4QQW7 gi|67678443 5 5 171 142 c, polypeptide 7 49 Cytochrome P450-like Q5EB99 gi|62078537 4437 7596241211 7.40 50 DnaJ homolog subfamily C member 3 Q9R0T3 gi|73620810 3 3 6 3 101 97 2.31 2.01 Dolichyl-diphosphooligosaccharide-- 51 protein glycosyltransferase 63 kDa P25235 gi|38051929 4 3 3 3 83 77 4.48 4.19 subunit [Precursor] Dolichyl-diphosphooligosaccharide-- 52 protein glycosyltransferase 67 kDa P07153 gi|132560 6 5 7 4 196 183 8.01 8.00 subunit [Precursor] Dolichyl-di-phosphooligosaccharide- 53 Q641Y0gi|519803374154 2 51506059 1.40 protein glycotransferase Endoplasmic reticulum protein ERp29 54 P52555 gi|2507015 2 4 3 37 2.00 2.00 [Precursor] P14625 55 Endoplasmin [Precursor] gi|15010550 8 11 351 4.00 human 56 Esterase 2 Q5I0K0 gi|56972413 4 8 72 168 57Fatty aldehyde dehydrogenase P30839gi|399362869754681251202152044.574.1110.9610.16 58 Fatty-acid amide hydrolase P97612 gi|6225312 4 3 55 52 59 Glucose-6-phosphatase P43428 gi|567864 1 1 3 1 60 60 2.00 2.00 60 Lipid phosphate phosphohydrolase 3 P97544 gi|1684745 1 1 2 2 60 59 2.00 2.00 61Liver carboxylesterase 1 [Precursor]P10959gi|46876644886 77125992001683.05 6.116.09 62Liver carboxylesterase 3 [Precursor]Q63108gi|249438565985598124853183171.532.1213.949.78 63Liver carboxylesterase 4 [Precursor]Q64573gi|5504186699 897658285249 10.0314.13 64 Liver carboxylesterase B-1 [Precursor] Q63010 gi|2494387 7 7 11 9 7 7 94 61 178 146 9.43 2.00 65 Lrpap1 protein [Fragment] Q642A1 gi|51980664 3 55 66 Mannosyl-oligosaccharide glucosidase O88941 gi|48427849 1 1 2.00 1.30 Membrane-bound transcription factor 67 Q9WTZ3 gi|17367438 4 3 7 6 46 46 2.02 2.01 site-1 protease [Precursor] Mid-1-related chloride channel 2; Mid- Q8VIF1 gi|17736804 68 1-related chloride channel 1; Q9WU61 gi|14278955 243 LOC170927 protein Q66HQ5 gi|51858922 69 NADH-cytochrome b5 reductase P20070 gi|38303959 53223343103851501433.652.522.282.09 70 NADPH--cytochrome P450 reductase P00388 gi|127966 6 11 10 5 2 9 8 46 340 358 2.04 2.01 8.32 6.68 Neutral alpha-glucosidase AB Q8BHN3 71 gi|2104689 5 6 6 4 7 78 131 124 3.05 4.69 [Precursor] mouse 72 Nicalin [Precursor] Q5XIA1 gi|67460594 3 1 3 1 54 54 2.01 1.70 Peptidyl-prolyl cis-trans isomerase B 73 P24368 gi|46397778 5 5 6 4 56 211 2.88 1.92 [Precursor] 74 PRA1 family protein 3 Q9ES40 gi|38494360 2 1 1 1 48 48 1.30 1.70 75 Protein disulfide-isomerase [Precursor] P04785 gi|56872 18 17 20 20 16 15 17 16 428 297 694 634 13.96 11.64 26.07 23.40 Protein disulfide-isomerase A3 76 P11598 gi|62650967 16 17 20 20 13 12 21 19 337 264 704 622 13.60 12.27 32.42 29.67 [Precursor] Protein disulfide-isomerase A4 77 P38659 gi|393203 4 3 11 10 13 10 60 60 346 327 14.61 13.42 [Precursor] Protein disulfide-isomerase A5 78 Q5I0H9 gi|62286967 6 6 9 4 75 71 4.98 4.28 [Precursor] Protein disulfide-isomerase A6 79 Q63081 gi|488838 8 8 9 7 323 308 12.05 11.73 [Precursor] 80 Reg receptor Q9JMA8 gi|7339684 4 3 5 1 50 50 2.01 2.00 Sarcoplasmic/endoplasmic reticulum 81 Q64578 gi|9789714 7 3 53 53 calcium ATPase 1 Sarcoplasmic/endoplasmic reticulum 82 P11507 gi|114315 9 5 6 4 85 78 6.00 4.19 calcium ATPase 2 Sarcoplasmic/endoplasmic reticulum 83 P18596 gi|114316 3 53 calcium ATPase 3 Q6NZC7 84 SEC23-interacting protein gi|55583895 3 40 mouse similar to alpha glucosidase II, beta 85 - gi|62653339 6 6 5 156 138 6.96 subunit 86similar to binding protein - gi|6264180812451 4656561531381.40 6.006.04 similar to Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha- 87 - gi|62644726 2 3 4 91 87 2.65 mannosidase (ER alpha-1,2- mannosidase) 88 similar to Exostosin 2 - gi|62645426 5 4 6 5 115 133 6.01 6.86 similar to Microsomal triglyceride 89 - gi|348607893366348976991152382.022.636.0111.71 transfer protein similar to Transmembrane emp24 90 - gi|27697481448634883993384594344.004.008.017.71 protein transport domain containing 4 similar to transmembrane emp24 91 - gi|62664383776777895495246296047.308.5611.4013.01 protein transport domain containing 7 Soluble calcium-activated nucleotidase 92 Q8K4Y7 gi|71153846 7 6 15 13 4 3 16 13 99 75 602 542 3.14 2.70 25.42 24.70 1 93 Sterol 12alpha-hydroxylase P450 Q9WVT5 gi|13676851 3 2 121 4.00 Sterol regulatory element binding 94 P56720 gi|17380503 5 4 3 40 2.01 2.00 protein 1 [Fragment] 95 Tapasin Q99JC6 gi|38541036 1 1 2 4 110 108 2.02 2.02 Transitional endoplasmic reticulum 96 P46462 gi|38014694 9 12 20 20 7 5 22 19 116 90 493 459 4.40 3.82 28.87 26.64 ATPase 97 Translocon-associated protein delta Q07984 gi|34849863 2 1 1 1 43 43 2.00 2.00 subunit [Precursor] UDP-glucose:glycoprotein 98 Q9JLA3gi|680529863163 11354545757 2.191.31 glucosyltransferase 1 [Precursor] 99 Unknown (protein for MGC:125054) - gi|78394967 3 4 33 93 P59481 100 VIP36-like protein [Precursor] gi|29611880 3 41 mouse 101 Xylosyltransferase 2 Q9EPI0 gi|71164811 4 5 7 5 211 200 6.12 6.04

Unknown 1 Ab2-417 Q7TMC7 gi|33086660 19 545 2 Ac2-233 Q7TPJ1 gi|32527749 8 72 3 Ac2-248 Q7TPI9 gi|32527753 2 4 61 6.00 gi|63650368 4 cDNA sequence BC048507 - 248 mouse Q9Y390 5 CGI-81 protein gi|4929631 1 54 human 6 Deleted in polyposis 1-like 1 Q5XI60 gi|54035487 2 2 72 2.47 gi|51458852 7 DKFZP564C196 protein (predicted) - 11.70 human family with sequence similarity 20, 8 - gi|62657273 4 5 5 2 2 3 66 61 98 2.00 2.00 2.86 member A (predicted) family with sequence similarity 20, 9 - gi|62658545 2 4 3 85 109 2.05 member C (predicted) 10 Hypothetical LOC312135 Q5PQM0 gi|56268908 4 3 45 79 4.85 11 Hypothetical LOC363016 Q5U2Q3 gi|55249800 2 49 12 Hypothetical protein Q3KR93 gi|76780097 2 3 35 2.00 13 Hypothetical protein Q5BK43 gi|60551444 1 1.70 14 Hypothetical protein Q3KRE2 gi|77415399 3 2 83 2.03 15 Hypothetical protein Q3MIE5 gi|75517318 7 5 54 54 16 Hypothetical protein Q3B8Q2 gi|77748037 2 2 57 68 17 Hypothetical protein Q5I0M3 gi|56971788 2 45 18 Hypothetical protein [Fragment] Q6GX83 gi|48686592 4 1.31 Hypothetical protein 19 Q68DY6 gi|51476188 1 73 DKFZp686B09139 20 Hypothetical protein LOC498266 Q6AYB8 gi|50925699 4 6 7 7 126 236 8.02 10.23 21 hypothetical protein LOC500282 - gi|66730258 1 52 22 Hypothetical protein MGC116126 Q4QQU5 gi|67678472 1 57 23 Hypothetical protein MGC124555 Q3MID6 gi|75516455 3 2 5 58 58 1.41 24 Hypothetical protein MGC124825 Q3T1I4 gi|74353811 3 4 218 5.30 Hypothetical protein 25 Q5RJR8 gi|55778335 4 43 RGD1305092_predicted Hypothetical protein 26 Q562C4 gi|62531324 5 6 108 4.43 RGD1305205_predicted Hypothetical protein 27 Q5BK17 gi|60688195 2 2 82 2.47 RGD1309288_predicted Hypothetical protein 28 Q499P3 gi|71121767 2 2 1 3 78 107 1.70 2.00 RGD1311230_predicted 29 hypothetical protein XP_217094 - gi|27719651 3 3 159 4.47 30 hypothetical protein XP_219337 - gi|62641295 1 1 55 2.00 31 hypothetical protein XP_578521 - gi|62650311 2 1.30 32 hypothetical protein XP_579846 - gi|62662981 1 1.30 33 LOC170824 protein Q5RKL5 gi|55715850 5 3 86 3.31 34 LRRGT00013 Q6TXI6 gi|37654242 6 3 54 2.00 35 LRRGT00110 Q6TUD4 gi|56268893 4 5 4 5 110 169 3.54 5.34 Q6A0B9 36 MKIAA0139 protein [Fragment] gi|74188812 2 52 mouse Q80U00 37 MKIAA0454 protein [Fragment] gi|28972229 2 43 mouse Q86WR7 38 Protein C10orf47 gi|73620073 5 1.40 human 39 RGD1310494_predicted protein Q497B0 gi|72679567 1 1 59 2.00 40 RGD1311026_predicted protein Q4KLZ6 gi|68533714 5 5 191 10.00 41 RGPR-p117 Q75N33 gi|47076880 9 10 198 12.40 gi|63641883 42 RIKEN cDNA 3110004L20 - 269 mouse 43 similar to 1110065L07Rik protein - gi|62662993 1 2 53 1.71 44 similar to 1810073N04Rik protein - gi|62657470 7 14 11 45 330 13.95 45 similar to 5730455P16Rik protein - gi|62656640 1 1 63 2.00 46 similar to 6330579B17Rik protein - gi|34870890 5 1.41 47 similar to 9130011E15Rik protein - gi|62642398 2 2.00 48 similar to Ab2-095 - gi|62654095 6 9 9 51 139 10.20 49similar to C530043G21Rik protein - gi|626595533456218967632522951.411.3011.7014.61 similar to chromosome 19 open reading gi|73987359 50 - 373 frame 10 dog similar to expressed sequence 51 - gi|62664513 6 2.02 AI173486 similar to Expressed sequence 52 - gi|62660356 2 2 161 2.00 AI788959 similar to Expressed sequence 53 - gi|62649653 2 2.00 AU040320 54 similar to FLJ16237 protein - gi|62650633 1 65 55 similar to hypothetical protein - gi|62638447 2 140 56 similar to hypothetical protein - gi|62718515 2 51 57 similar to hypothetical protein - gi|62658093 5 174 similar to hypothetical protein 58 - gi|62662365 1 58 6030458H05 similar to hypothetical protein 59 - gi|62656475 3 1.31 FLJ10156 similar to hypothetical protein 60 - gi|62645841 2 45 FLJ14681 similar to Hypothetical protein 61 - gi|62663362 2 1.31 MGC38211 similar to hypothetical protein 62 - gi|62664164 3 3 103 4.85 MGC5391 63 similar to ICBP90 binding protein 1 - gi|62665711 4 2.00 64 similar to mKIAA0002 protein - gi|34867525 6 3 4 2 81 81 1.44 1.33 65 similar to mKIAA0051 protein - gi|62640787 4 98 66 similar to mKIAA0493 protein - gi|62652461 7 11 62 2.94 67 similar to Protein KIAA0494 homolog - gi|62649446 1 2.00 similar to putative protein product of 68 - gi|62661643 3 3 51 2.00 HMFN0672 69 similar to R31546_1 - gi|62651797 5 1.41 70 similar to RIKEN cDNA 1300017J02 - gi|62654202 4 5 122 6.01 71 similar to RIKEN cDNA 1700013B16 - gi|62663161 7 7 127 6.49 72 Similar to RIKEN cDNA 1810013B01 Q6DGG1 gi|49904636 1 1 2 33 2.00 3.30 73 similar to RIKEN cDNA 1810036I24 - gi|34861791 2 2 3 2 55 55 2.00 2.00 74 similar to RIKEN cDNA 1810037C20 - gi|62667553 2223 345442218223 4.006.00 75 Similar to RIKEN cDNA 2210404D11 Q5BK32 gi|60552734 1 51 76 similar to RIKEN cDNA 2310008M10 - gi|62644383 2 1.70 77 Similar to RIKEN cDNA 2310034L04 Q5M7T4 gi|81883039 3 3 2 3 96 140 2.03 5.70 78 similar to RIKEN cDNA 2310046O06 - gi|34863505 1 2 51 1.70 79 similar to RIKEN cDNA 2510039O18 - gi|34872456 2 4 4 51 130 6.85 80 similar to RIKEN cDNA 2900024C23 - gi|62660036 4 4 117 6.89 81 similar to RIKEN cDNA 3110023G01 - gi|62664683 3 53 82 similar to RIKEN cDNA 5730596K20 - gi|62641830 2 3 75 1.31 83 similar to RIKEN cDNA 6330407D12 - gi|62647229 2 2 2 48 123 4.00 84 Similar to RIKEN cDNA 6330409N04 Q5M7T2 gi|81883037 2 45 85 similar to RIKEN cDNA 8030451K01 - gi|62643445 2 1 58 2.00 86 similar to RIKEN cDNA A930025J12 - gi|62645640 2 3 77 2.47 87 similar to RIKEN cDNA B230339H12 - gi|62662951 1 1 43 1.30 88 similar to RIKEN cDNA C730027E14 - gi|62656367 3 3 2 45 103 4.00 89 similar to WD repeat domain 11 - gi|62641380 3 2.00

Endosomal Transmembrane 9 superfamily protein 1 Q66HG5gi|622875478898888734931734333813.7412.697.527.40 member 2 [Precursor]

Lysosomal P35475 1 Alpha-L-iduronidase [Precursor] gi|547707 3 32 human Alpha-N-acetylgalactosaminidase 2 Q66H12 gi|67460657 2 2 3 67 62 4.00 [Precursor] Beta-hexosaminidase alpha chain 3 Q641X3 gi|51980341 5 6 2.12 2.23 [Precursor] 4 Cathepsin B [Precursor] P00787 gi|1705630 1 1 2 2 39 38 1.98 1.80 5 Cathepsin D [Precursor] P24268 gi|55882 3 3 8 6 115 107 5.12 4.92 6 Cathepsin H [Precursor] P00786 gi|115729 2 2 4 3 75 70 2.59 2.50 7 Cathepsin L [Precursor] P07154 gi|55888 1 5 5 8 8 34 191 219 10.97 10.11 Cation-dependent mannose-6- 8 Q6AY20 gi|50927031 3 3 3 3 2 2 53 79 147 1.34 2.00 4.00 phosphate receptor 9 Di-N-acetylchitobiase [Precursor] Q01460 gi|399377 1 1 2 1 42 42 2.00 1.70 10Dipeptidyl-peptidase I [Precursor] P80067gi|25520922432254666368693.703.706.016.01 Lysosomal acid phosphatase 11 P20611 gi|130729 2 3 2 3 3 38 62 62 2.02 1.34 [Precursor] 12 Lysosomal membrane glycoprotein 2 Q6P6W1 gi|38303859 1 52 13 Lysosome membrane protein II P27615 gi|38197654 1 1 1 1 75 75 2.00 2.00 Lysosome-associated membrane 14 P14562 gi|56578 1 1 46 46 glycoprotein 1 [Precursor] Lysosome-associated membrane 15 P17046 gi|126382 1 2 2 52 2.00 2.00 glycoprotein 2 [Precursor] Mannose 6-phosphate/insulin-like 16 Q63002 gi|1398935 7 8 4.03 3.74 growth factor II receptor 17 N-acylsphingosine amidohydrolase 1 Q6P7S1 gi|81885370 4 1.41 Palmitoyl-protein thioesterase 1 18 P45479 gi|1172592 2 2 4 2 76 76 2.01 2.00 [Precursor] Protective protein for beta- 19 Q6AYS3 gi|50925541 5 4 135 6.00 galactosidase 20 Ribonuclease 4 [Precursor] [Fragment] Q9R132 gi|5802394 1 1.40 Sphingomyelin phosphodiesterase 1, 21 Q5XIA6 gi|53734276 1 2 4 2 46 46 2.00 2.00 acid lysosomal Tartrate-resistant acid phosphatase type 22 P29288 gi|130723 2 1 2.00 1.31 5 [Precursor] 23Tripeptidyl-peptidase I [Precursor] Q9EQV6gi|137862062121 1152526060 2.002.00

Plasma membrane 1 Anion exchange protein 3 P23348 gi|114782 4 3 1.41 1.31 2 Asialoglycoprotein receptor 1 P02706 gi|202988 2 4 4 6 5 55 164 147 8.00 7.70 3 Asialoglycoprotein receptor 2 P08290 gi|126136 4 4 5 4 41 45 1.84 1.31 4 Band 3 anion transport protein P23562 gi|20141169 2 4 1 35 2.01 1.70 5Basigin [Precursor] P26453gi|579084322 1191819092 2.002.00 Q9WVT6 6 Carbonic anhydrase 14 [Precursor] gi|8928038 1 1 41 1.40 mouse 7 Epidermal growth factor receptor Q9QX70 gi|6478868 9 7 7 5 155 150 8.00 7.00 8 Ezrin P31977 gi|40804381 3 4 56 61 9 Growth hormone receptor [Precursor] P16310 gi|121183 1 1 2.00 2.00 Low-density lipoprotein receptor 10 P35952 gi|547842 4 10 7 2.98 2.49 [Precursor] O88495 11 Melatonin-related receptor gi|6016576 1 34 mouse 12 MHC class Ia protein O19446 gi|9755497 2 5 2 99 162 4.00 13 MHC class Ib alpha chain [Fragment] O62934 gi|3006074 2 56 14 MHC class Ib antigen [Fragment] Q6SY93 gi|42516524 2 67 15 Neu protooncoprotein Q8K3F9 gi|81866669 2 2 67 67 16 Nucleoside diphosphate kinase B P19804 gi|127984 2 3 61 2.00 Ras-related C3 botulinum toxin 17 Q6RUV5 gi|51701705 3 4 3 3 106 107 3.00 3.03 substrate 1 Receptor tyrosine-protein kinase erbB- 18 Q62956 gi|21431759 3 67 4 [Precursor] Related RAS viral (R-ras) oncogene 19 Q5BJU0 gi|81882523 3 3 3 64 64 2.00 homolog 2 20 RT1.A1(F) protein [Fragment] Q31257 gi|1483574 4 5 123 10.00 similar to Transferrin receptor protein 2 21 - gi|62658612 3 2 4 1 70 70 2.00 2.00 (TfR2) Sodium/potassium-transporting 22 P06686 gi|114379 4 6 4 34 89 92 ATPase alpha-2 chain [Precursor] Solute carrier family 2, facilitated 23 P12336gi|12175822222 22625460482.00 4.003.70 glucose transporter member 2 24 Solute carrier family 23 member 1 Q9WTW7 gi|24212394 5 3 5 47 47 2.13 25 Stabilin-2 [Precursor] [Fragment] Q8CFM6 gi|24285893 4 2 11 8 73 73 2.12 2.10 26 Syndecan-4 [Precursor] P34901 gi|464749 2 2 32 2.00 27 System N amino acid transporter 1 Q9JHZ9 gi|51859110 2 2 4 2 53 53 2.00 2.00 Vacuolar ATP synthase catalytic P38607 28 gi|586208 4 2 77 78 subunit A, osteoclast isoform human

Cargo 17-beta hydroxysteroid dehydrogenase 1 Q5M875 gi|77416416 6 6 211 7.01 13 [Precursor] 2 Aa1064 Q7TMA5 gi|32492562 24 23 41 16 24 46 210 161 1203 5.14 10.50 61.64 3 Aa2-001 Q7TP83 gi|33086498 1 2 1 1 5 54 56 2.00 2.00 2.00 4 Ac1262 Q7TMA9 gi|33086642 4 5 7 93 375 4.02 Adipocyte-derived leucine 5 Q9JJ22 gi|8131850 3 2 4 2 46 46 2.01 2.00 aminopeptidase [Precursor] 6Afamin [Precursor] P36953gi|5437936454337654501631652.132.008.008.00 7 Alpha-1-antiproteinase [Precursor] P17475 gi|112889 7 7 10 10 7 7 10 9 251 187 359 309 9.28 6.61 11.99 12.17 8 Alpha-1-inhibitor 3 [Precursor] P14046 gi|112893 32 32 34 34 28 25 37 32 676 519 1485 1429 30.70 25.86 51.32 48.67 9 Alpha-1-macroglobulin Q63041 gi|202857 11 8 21 10 24 110 162 747 5.58 32.00 10Alpha-2 antiplasmin Q80ZA3gi|289328164355 645151130207 6.017.70 11Alpha-2-HS-glycoprotein [Precursor]P24090gi|2063151098988894183765024346.105.4614.3212.99 12 Alpha-2-macroglobulin [Precursor] P06238 gi|71051900 4 2 2 3 4 3 74 41 68 2.01 4.59 1.71 P02662 13 Alpha-S1-casein [Precursor] gi|115646 5 3 4.04 4.01 (bovin) 14AMBP protein [Precursor] Q64240gi|56972076556644651971681751647.407.006.066.02 15 Angiopoietin-like 3 Q5I0L8 gi|56971793 2 4 4 4 44 79 2.00 4.23 16Angiotensinogen [Precursor] P01015gi|5658507454554455108972552183.022.4610.009.70 17 Anionic trypsin I [Precursor] P00762 gi|57408 1 1 59 44 18 Apolipoprotein A-I [Precursor] P04639 gi|55747 4 4 8 6 116 108 8.13 8.09 19 Apolipoprotein A-II [Precursor] P04638 gi|55749 5 5 6 7 168 162 10.05 8.33 20 Apolipoprotein A-IV [Precursor] P02651 gi|202950 3 13 13 14 14 46 585 559 25.03 20.92 21 Apolipoprotein A-V [Precursor] Q9QUH3 gi|60391723 4377228869662922752.012.019.649.76 22 Apolipoprotein C-I [Precursor] P19939 gi|71051103 2 2 3 50 50 1.98 23 Apolipoprotein C-III [Precursor] P06759 gi|6226553 1 2 3 1 2 3 268 35 233 2.00 2.92 4.12 24 Apolipoprotein E [Precursor] P02650 gi|1703338 13 13 21 20 14 13 22 20 367 266 846 710 14.58 13.72 30.81 29.74 25 Apolipoprotein F [Precursor] Q5M889 gi|33086636 4 2 3 3 98 99 4.00 4.00 Q9CXI5 26 ARMET protein [Precursor] gi|23396453 2 2 3 2 118 115 4.00 3.70 mouse 27Beta-2-glycoprotein I [Precursor] P26644gi|135195469567799101100981252.063.817.428.44 28 Beta-2-microglobulin [Precursor] P07151 gi|114778 1 2 1 38 1.40 1.30 29 B-factor, properdin Q6MG74 gi|46237594 6 8 234 8.01 C4b-binding protein alpha chain 30 Q63514 gi|2493792 2 2 5 2 50 50 2.01 2.01 [Precursor] 31 C8b protein [Fragment] Q5EB58 gi|59808937 2 2 4 2 65 65 2.00 2.00 32 Carboxypeptidase B2 [Precursor] Q9EQV9 gi|62899668 3 3 2 60 58 2.28 33 Cathepsin Z [Precursor] Q9R1T3 gi|34978341 2 3 37 1.44 34 Ceruloplasmin [Precursor] P13635 gi|554429 6 18 16 4 3 15 14 43 654 613 2.59 2.22 24.60 23.10 35 Clusterin [Precursor] P05371 gi|57241 10 8 11 9 6 5 12 10 140 116 237 244 5.75 3.92 14.01 13.71 36 Coagulation factor IX [Fragment] P16296 gi|119776 3 2 2.00 2.00 37 Coagulation factor X [Precursor] Q63207 gi|48427854 3 35 38 Coagulation factor XII Q5M879 gi|56789277 1 4 5 5 38 110 2.60 7.00 39 Collagen alpha1 [Fragment] Q63079 gi|2894106 6 8 2.12 2.02 Complement C1r-A subcomponent Q8CG16 40 gi|47605363 2 4 47 2.01 [Precursor] mouse Complement C1s subcomponent 41 Q6P6T1 gi|76364096 3 2 2 2 103 108 4.00 3.30 [Precursor] 42 Complement C3 [Precursor] P01026 gi|116597 39 41 39 43 39 33 40 40 863 650 1642 1602 25.39 20.91 58.65 57.21 43 Complement C4 [Precursor] P08649 gi|29337194 4 10 10 21 12 35 351 314 17.53 16.23 44 Complement C5 [Fragment] P08650 gi|46397770 1 1 48 48 45 Complement component 2 Q6MG73 gi|46237595 1 2 8 2 49 49 2.02 2.00 46 Complement component 4, gene 1 Q6MG79 gi|46237589 6 111 Complement component C9 47 Q62930gi|24994674376 777371208183 11.409.18 [Precursor] 48 Complement factor H-related protein Q91WX0 gi|62659431 2 1 54 2.00 Contrapsin-like protease inhibitor 1 49 P05545gi|220698879877882832945976284.126.906.367.93 [Precursor] Contrapsin-like protease inhibitor 3 50 P05544 gi|2507387 9 13 9 13 305 803 13.21 18.97 [Precursor] Contrapsin-like protease inhibitor 6 51 P09006gi|50927309889978993062635224579.023.8116.009.70 [Precursor] 52 C-reactive protein [Precursor] P48199 gi|1345834 2 2 2 3 3 124 452 4.00 3.30 4.00 Q07507 53 Dermatopontin [Precursor] gi|311614 1 3 61 2.00 human 54Fetuin-B [Precursor] Q9QX79gi|11131967999998971761392702727.176.4010.709.87 55 Fibrinogen alpha chain [Precursor] P06399 gi|790486 11 9 11 12 10 6 18 14 184 156 470 443 6.46 3.90 16.43 16.13 56 Fibrinogen beta chain [Precursor] P14480 gi|170680 6 9 9 4 11 11 36 397 392 1.71 19.82 19.03 57Fibrinogen gamma chain [Precursor]P02680gi|118393735784471153771852964.043.889.9915.46 58 Fibrinogen, gamma polypeptide Q68FY3 gi|51259324 3 130 59 Fibronectin [Precursor] P04937 gi|120178 9 9 14 10 290 260 11.42 11.00 Glycosylphosphatidylinositol 60 Q8R2H5 gi|20152555 8 3 4 3 48 58 2.02 4.00 phospholipase D [Fragment] 61 Haptoglobin [Precursor] P06866 gi|123513 9 11 15 10 12 13 16 223 383 525 637 8.28 11.62 20.08 24.74 62 Hemopexin [Precursor] P20059 gi|204621 12 11 13 13 10 9 12 11 179 155 431 386 6.13 5.09 17.83 14.80 63 Heparin cofactor II [Precursor] Q64268 gi|2500775 2 1 1 5 3 35 55 55 2.01 2.00 Hepatic triacylglycerol lipase 64 P07867 gi|126310 1 2 1 2 2 34 53 53 2.92 2.48 [Precursor] 65Hepcidin [Precursor] Q99MH3gi|215420702122 225656147136 4.003.70 66 Hypothetical protein Q5RK13 gi|55778418 3 1 56 58 Hypothetical protein Q68DT4 67 gi|51476292 5 160 DKFZp686F10164 human Insulin-like growth factor binding 68 P21744gi|1240673343 435957116119 5.404.48 protein 4 [Precursor] Insulin-like growth factor binding 69 Q5RJM3 gi|55824772 3 3 2 2 42 82 2.00 3.00 protein 7 70 Insulin-like growth factor I [Precursor] P08025 gi|124262 3 2 3 3 60 58 2.05 1.71 Inter-alpha-trypsin inhibitor heavy 71 Q63416 gi|602886 3 3 10 7 3 2 9 5 66 61 122 107 2.01 1.70 7.11 4.46 chain H3 [Precursor] 72 Kininogen-1 [Precursor] P08934 gi|125508 5 3 4 3 115 111 4.54 4.47 P08071 73 Lactotransferrin [Precursor] gi|21431833 11 2.05 mouse Lipopolysaccharide-binding protein 74 Q63313 gi|2497617 2 2 2 1 71 71 2.00 2.00 [Precursor] Liver regeneration-related protein 75 Q7TNX0 gi|33187764 23 20 23 19 509 546 22.24 27.78 LRRG03 76 LOC314521 protein Q569B3 gi|62201965 2 1 52 2.00 77 LRRGT00077 Q6TUG7 gi|37361840 2 67 Q924C6 78 Lysyl oxidase homolog 4 [Precursor] gi|20177956 3 33 mouse Mannose-binding protein associated 79 serine protease-1 [Precursor] Q9JJS9 gi|7688073 2 1 2 39 2.00 2.00 [Fragment] MIR-interacting saposin-like protein Q9QXT0 80 gi|14198401 3 3 3 1 67 67 2.00 2.00 [Precursor] mouse 81 Murinoglobulin 2 Q6IE52 gi|47169516 9 8 21 10 24 124 248 831 2.00 2.01 82 Plasma alpha-L-fucosidase [Precursor] Q6AYS4 gi|50927663 4 1 1 35 2.00 1.70 83 Plasma kallikrein [Precursor] P14272 gi|125186 4 1.70 Plasma retinol-binding protein 84 P04916gi|1324074454434475551751413.043.398.008.00 [Precursor] 85Plasminogen [Precursor] Q01177gi|5295890107999612102221842962514.054.1012.3712.58 Polymeric-immunoglobulin receptor 86 P15083gi|13020199551089826520219118712.076.689.307.91 [Precursor] 87 Protein C10orf58 homolog [Precursor] Q6AXX6 gi|73620083 2 1 2 2 62 62 2.00 1.70 88 Protein C19orf10 homolog [Precursor] Q9CPT4 gi|61221740 2 2 3 3 4 3 43 73 2.01 2.01 2.57 2.49 mouse 89 Protein FAM55D [Precursor] Q5XI89 gi|53733569 13 11 14 14 11 10 14 14 458 352 470 413 13.82 12.27 22.12 21.11 90 Prothrombin [Precursor] P18292 gi|56970 6 6 12 10 10 7 12 10 127 104 448 439 4.72 3.35 18.23 16.70 91 PRx IV Q9Z0V5 gi|37590233 4 3 81 75 92Ribonuclease 4 [Precursor] O55004gi|39148034444225564602582491.811.536.266.23 Q8VC96 93 RIKEN cDNA 1300017J02 gi|18204720 5 76 mouse 94Secreted phosphoprotein 24 Q62740gi|24989403333222273661011062.031.334.004.00 95 Selenoprotein P [Precursor] P25236 gi|134424 1 1 1 1 78 78 2.00 1.70 Serine protease inhibitor A3M 96 Q63556 gi|57296 8 8 6 7 431 376 10.28 10.04 [Precursor] [Fragment] Serine/cysteine proteinase inhibitor, 97 Q5M7T5 gi|56789738 3 6 5 61 119 2.00 clade C, member 1 98 Serotransferrin [Precursor] P12346 gi|6175089 25 2 20 20 22 19 570 54 582 512 25.67 27.67 99 Serum albumin [Precursor] P02770 gi|113580 35 35 24 24 32 29 21 22 2496 2130 2610 2360 45.49 43.06 34.63 32.01 Serum amyloid P-component 100 P23680 gi|3183550 1 1 55 42 [Precursor] 101Serum paraoxonase/arylesterase 1 P55159gi|1945471332233321451321051054.003.704.004.00 102Serum paraoxonase/lactonase 3 Q68FP2gi|512610612244 645146139128 8.007.30 similar to Complement C5 precursor 103 - gi|62644999 2 66 (Hemolytic complement) similar to Complement component 1, r 104 - gi|62648141 3 3 90 3.70 subcomponent similar to inter-alpha trypsin inhibitor, 105 - gi|62662177 3 6 5 5 100 141 2.96 5.12 heavy chain 1 similar to inter-alpha-inhibitor H2 106 - gi|62663812 7 6 9 7 170 198 8.05 7.72 chain 107 similar to RIKEN cDNA 1700013L23 - gi|62644736 2 2.49 Q8VIM6 108 Stereocilin [Precursor] gi|47606191 4 63 mouse 109 Stromelysin-3 [Precursor] Q499S5 gi|78099008 1 1.40 110Sulfated glycoprotein 1 [Precursor] P10960gi|69814243353 4356569183 4.003.70 T-cell immunomodulatory protein 111 Q8R4E1 gi|45477218 1 1 2.00 2.00 [Precursor] 112 T-kininogen I [Precursor] P01048 gi|60392582 4 7 6 40 263 10.36 113 T-kininogen II [Precursor] P08932 gi|60392583 6 5 4 68 52 111 114 TPA regulated locus Q4V899 gi|66911475 3 3 3 3 57 91 2.12 4.03 115 TRANSFERRIN homolog Q9DBD0 gi|12836677 5 2.01 116 Urinary protein 2 [Precursor] P81828 gi|6226289 2 1 98 86 117 Vitamin D-binding protein [Precursor] P04276 gi|203927 13 11 12 13 11 10 12 12 340 303 541 516 10.98 9.82 18.30 16.63 Vitamin K-dependent protein C 118 P31394 gi|56963 3 3 4 4 235 212 6.00 6.00 [Precursor] 119Vitronectin Q62905gi|12550441336 244345894191 2.094.017.30 120 Zinc-alpha-2-glycoprotein [Precursor] Q63678 gi|620121 1 1 1 1 52 52 2.00 2.00

Localization undetermined 15 days pregnant adult female placenta Q91X78 1 cDNA, RIKEN full-length enriched gi|74225814 3 2 50 50 mouse library, clone:I530023A18 product 1-phosphatidylinositol-4,5- 2 O89040 gi|32699411 4 33 bisphosphate phosphodiesterase beta 2 2-hydroxyacylsphingosine 1-beta- 3 Q09426 gi|1168907 1 34 galactosyltransferase precursor 4 60S acidic ribosomal protein P1 P19944 gi|133053 1 40 5 60S acidic ribosomal protein P2 P02401 gi|133063 4 4 4 3 148 130 6.00 4.85 6 60S ribosomal protein L10 Q6PDV7 gi|50403574 2 2 3 3 75 75 2.00 2.00 7 60S ribosomal protein L12 P23358 gi|132653 1 36 8 60S ribosomal protein L13a P35427 gi|548747 2 2 1 2 44 2.00 2.00 9 60S ribosomal protein L15 P61314 gi|47117719 4 3 44 44 10 60S ribosomal protein L22 P47198 gi|1172995 2 2 1 1 92 92 2.00 2.00 11 60S ribosomal protein L23a P62752 gi|51338615 3 3 3 2 72 80 2.00 2.00 12 60S ribosomal protein L26 P12749 gi|132827 1 3 2 54 2.58 2.09 13 60S ribosomal protein L5 P09895 gi|1173056 4 4 3 3 158 145 6.00 6.00 14 60S ribosomal protein L7a P62425 gi|54039228 6 7 4 5 95 90 4.01 4.01 15 60S ribosomal protein L9 P17077 gi|133033 4 4 84 82 16 Aa2-111 Q7TP82 gi|33086502 16 18 14 20 515 772 5.94 4.41 17 Ac2-190 Q7TPJ5 gi|32527741 6 6 4 68 82 4.18 18 Acetylcholinesterase Q505J2 gi|63101489 2 33 19 Acetyl-CoA transporter Q9JM68 gi|7768591 1 1.30 20 Actin-like protein 2 Q5M7U6 gi|62899645 4 3 4 2 73 71 4.00 4.00 Actin-related protein 2/3 complex 21 Q99PD4 gi|59797636 3 2 46 46 subunit 1A Actin-related protein 2/3 complex Q9JM76 22 gi|9790141 1 1 1 69 69 2.00 subunit 3 mouse Acyl-CoA synthetase isoform 6 23 Q6IU14 gi|48256734 9 39 variant2 24 Acyl-CoA-binding protein P11030 gi|54261671 3 3 64 62 25 Aldehyde dehydrogenase 3B1 Q5XI42 gi|67460109 4 3 52 52 Aldehyde dehydrogenase family 7 26 Q64057 gi|25090044 1 41 member A1 [Fragment] 27 Aldehyde oxidase 1 Q5QE80 gi|55976808 3 42 P26232 28 Alpha-2 catenin gi|14916980 5 3 51 51 human 29 Alpha-2u globulin Q9JJI0 gi|204261 6 3 247 185 Anaphase promoting complex subunit Q9WVM3 30 gi|37537869 6 2.69 7 mouse 31 Annexin A5 P14668 gi|4033508 5 5 6 4 70 70 2.12 2.01 32 Argininosuccinate synthase P09034 gi|38648840 7 5 6 5 146 131 8.30 7.79 ATPase, H+ transporting, lysosomal 33 - gi|77627990 7 184 (vacuolar proton pump) noncat ATPase, H+ transporting, V0 subunit D 34 Q5M7T6 gi|81883040 5 4 4 4 113 109 6.00 5.71 isoform 1 Q80Y55 35 BSD domain containing 1 gi|74184251 2 1 52 2.00 mouse 36 Calponin-3 P37397 gi|38303945 3 3 6 4 54 54 1.40 1.32 37 Choline dehydrogenase Q6UPE0 gi|55250736 1 1.30 38 Complement inhibitory factor H Q91YB6 gi|15485713 9 8 166 7.71 39 Cystatin C [Precursor] [Fragment] P14841 gi|56541029 2 2 2 2 125 120 4.00 4.00 40 Cysteine sulfinic acid decarboxylase Q64611 gi|5714429 5 4 5 4 78 78 2.01 2.01 41 Da1-24 Q7TP05 gi|33086684 5 6 54 205 42 DAMP-1 protein Q811A2 gi|28070980 1 1 64 1.30 43 Dihydropyrimidinase Q63150 gi|51980286 2 2 3 3 59 59 2.01 1.71 Down-regulated in nephrectomized rat 44 Q6I7R1 gi|75773325 1 2 91 4.00 kidney #3 Ectonucleoside triphosphate 45 Q6P6S9 gi|38303951 1 2 91 2.00 diphosphohydrolase 5 46 EH-domain containing 1 (predicted) - gi|62641789 3 54 47 Endomannosidase Q5GF25 gi|48479684 4 3 58 2.56 Enoyl-Coenzyme A, hydratase/3- 48 hydroxyacyl Coenzyme A Q5EBD2 gi|59809132 2 1 91 2.00 dehydrogenase 49 Epsilon 1 globin O88752 gi|81886893 2 2 51 51 50 Erythroid spectrin beta Q6XDA0 gi|33303720 6 5 41 2.02 Estrogen receptor-binding-associated 51 Q5PQP2 gi|56268883 2 48 gene 9 52 fibrinopeptide A - gi|229210 1 1 47 2.00 53 fibrinopeptide B - gi|229196 1 1 1 1 53 114 2.00 2.00 54 Fibronigen-like protein Q8K583 gi|25282415 1 1 2 51 45 3.70 55 Fructose-1,6-bisphosphatase 1 P19112 gi|50925519 2 2 4 4 67 64 3.95 3.52 56 Fructose-bisphosphate aldolase A P05065 gi|39963644 2 54 57Fructose-bisphosphate aldolase B P00884gi|16196063466 764850384337 12.0011.70 58 GASZ Q8VHF9 gi|18389978 3 1.40 59 Genethonin 1 Q5FVN1 gi|58477757 2 3 115 4.00 60 Glucosidase, alpha; acid Q6P7A9 gi|38197416 4 2 1.40 1.30 Glycogen [starch] synthase, liver; P17625 gi|204430 61 4 2 45 45 Glycogen synthase Q99MF8 gi|13242186 62 Glycogen phosphorylase, liver form P09811 gi|47480059 8 6 6 4 130 117 6.54 5.02 63 Glycosyltransferase AD-017 Q6AYF6 gi|50926937 3 2.00 64 GM2 activator protein Q8CJH4 gi|25006237 1 1 2 42 69 3.22 65 GPI-anchored ceruloplasmin Q9JL97 gi|6970046 16 14 632 2.00 66 Guanidinoacetate N-methyltransferase P10868 gi|204436 1 1 2 1 76 76 2.00 1.70 Guanine nucleotide-binding protein 67 P54311 gi|984553 3 2 1 50 50 2.00 G(I)/G(S)/G(T) beta subunit 1 Guanine nucleotide-binding protein 68 P54313 gi|51338712 1 2.00 G(I)/G(S)/G(T) beta subunit 2 Guanine nucleotide-binding protein 69 P08753 gi|120997 2 56 G(k), alpha subunit 70 Heat shock 70 kDa protein 1A/1B Q07439 gi|55977739 6 3 104 103 71 Heat shock 70 kDa protein 1L P55063 gi|56757502 5 2 104 103 72 Heat shock protein 2 Q66HL1 gi|51858601 8 10 282 472 73 Heat shock-related 70 kDa protein 2 P14659 gi|56387 8 6 282 277 74 Hepatic protein EIIH Q6QMY6 gi|45479292 1 1.70 75 Histidine triad protein 4 [Fragment] Q8K3P7 gi|21654864 1 1.70 76 Histidine-rich glycoprotein 1 Q99PS8 gi|59808159 5 7 5 6 70 192 2.06 8.64 77 Histidine-rich glycoprotein 2 Q99PS7 gi|13358878 7 4 120 2.00 Hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme 78 A thiolase/enoyl-Coenzyme A Q5BIZ5 gi|60688124 2 55 hydratase (Trifunctional protein), alpha subunit 79 Hypothetical LOC313220 Q5FVR5 gi|58477126 2 1 46 2.00 80 Hypothetical LOC365972 Q68FT5 gi|5126126 2 3 54 62 81 Hypothetical protein Q5U211 gi|55562828 3 2 4 3 50 48 4.31 3.94 82 Ig gamma-2B chain C region P20761 gi|121055 2 2 3 4 55 55 2.02 2.02 inositol polyphosphate-5-phosphatase 83 - gi|62644779 3 2 3 10 6 10 46 46 67 90 4.56 9.58 E (predicted) 84 Integral membrane protein 2B Q5XIE8 gi|53734537 2 1 82 2.00 interferon gamma induced GTPase 85 - gi|62656110 3 2.23 (predicted) 86 Interferon inducible protein 1 Q6AYC2 gi|50925693 2 3 57 1.73 87 Kallistatin P97569 gi|1762152 2 2 4 62 142 3.70 88 Ketohexokinase Q02974 gi|50926155 2 1 43 43 89 Kininogen 1 Q5PQU1 gi|56270334 7 8 312 11.05 90 Lecithin:cholesterol acyltransferase O35849 gi|60688171 4 2.00 91 LIM homeobox protein 3 (predicted) - gi|62644770 4 6 4 9 79 277 2.53 9.32 92 Liver annexin-like protein Q9JLV0 gi|7108713 3 4 3 2 121 86 3.89 3.30 93 Liver regeneration protein lrryan Q7TMB9 gi|32563565 9 16 10 17 375 966 14.04 24.37 Liver regeneration-related protein 94 Q7TNW9 gi|33187771 2 2 82 2.03 LRRG07 95 LOC299567 protein [Fragment] Q5I0H8 gi|56972100 4 5 107 6.50 96 LRRGT00057 Q6TXE2 gi|37654330 6 83 97 LRRGT00065 Q6TUH9 gi|37361816 3 56 98 LRRGT00111 Q6TUD3 gi|37361908 3 5 3 3 101 96 4.00 4.00 99Major urinary protein [Precursor] P02761gi|2042617 336633323 1761858.617.166.006.00 100 Mesoderm development candiate 2 Q5U2R7 gi|55250764 1 3 70 2.00 Methionine adenosyltransferase I, 101 Q5FVU2 gi|58477110 5 6 122 9.00 alpha 102 Monoglyceride lipase Q8R431 gi|47116974 3 2 2 2 108 108 4.00 3.40 103 Myomegalin Q9WUJ3 gi|4761644 4 43 104 Myotubularin related protein 3 Q5PQT2 gi|56270344 3 5 4 61 2.05 4.02 NAD(P) dependent steroid 105 Q5PPL3 gi|56388600 3 4 3 39 81 3.39 dehydrogenase-like Q8BVW0 106 Neutral alpha-glucosidase C gi|48428061 2 35 mouse 107 Nitric oxide synthase 3 [Fragment] Q68GV6 gi|51243731 6 42 Nitric-oxide synthase, endothelial 108 Q62600 gi|26421745 6 2 42 42 [Fragments] NOD-derived CD11c +ve dendritic Q3U3R7 109 gi|74209304 4 1 54 2.00 cells cDNA mouse 110 PDZ protein Mrt1b Q8K4T6 gi|22324239 2 1.30 111 Phenylalanine-4-hydroxylase P04176 gi|129975 1 2 1 37 2.00 1.70 112 Phosphoinositide phosphatase SAC1 Q9ES21 gi|11095248 4 5 82 5.80 113 Picalm protein Q498N4 gi|71679761 2 73 114 Poly(RC) binding protein 3 Q6AY48 gi|50927011 3 53 115 Probable saccharopine dehydrogenase Q6AY30 gi|73919297 5 4 3 3 86 90 5.40 4.85 Proline-rich protein [Precursor] 116 Q63461 gi|206413 5 47 [Fragment] Proteasome (Prosome, macropain) 26S 117 Q4FZT9 gi|71051911 2 2 52 2.00 subunit, non-ATPase, 2 Q9CR89 118 PTX1 PROTEIN homolog gi|12835992 2 4 3 49 104 4.00 mouse Putative ATP-dependent RNA helicase P16381 119 gi|130256 7 70 PL10 mouse 120 Pyruvate kinase, isozymes M1/M2 P11980 gi|125601 6 2 2.02 2.01 121 ras homolog gene family, member G - gi|82524300 1 1.70 122 Ras-related protein Ral-A P63322 gi|54038996 1 56 123 Ras-related protein Ral-B P36860 gi|548672 3 3 2 56 2.00 2.00 Rat alpha(1)-inhibitor 3, variant I 124 Q03626 gi|55562 19 23 29 613 3.99 19.73 [Precursor] 125 Rdh2 protein Q6P6V2 gi|38303814 4 3 3 101 1.35 3.70 Retinoic acid receptor responder 126 Q5BK77 gi|60551830 3 1 2 33 60 2.00 (Tazarotene induced) 2 127 RIO kinase 2 Q5I0I1 gi|56971841 2 2.00 S-adenosylmethionine synthetase alpha 128 P13444 gi|127048 5 7 132 9.41 and beta forms 129 Selenium binding protein 2 Q8VIF7 gi|49256633 2 3 2 37 2.00 2.00 Serine (Or cysteine) proteinase 130 Q68FT8 gi|51259429 4 4 209 4.86 inhibitor, clade F, member 2 Serine (Or cysteine) proteinase 131 inhibitor, clade G (C1 inhibitor), Q6P734 gi|38197406 3 42 member 1 Serine protease inhibitor 2.1 132 P09005 gi|134483 7 8 447 417 [Fragment] similar to Acyl-CoA-binding protein 133 (ACBP) (Diazepam binding inhibitor) - gi|62659021 2 56 (DBI) (Endozepine) (EP) 134 similar to Aldh8a1 protein - gi|62638321 2 4 49 3.36 similar to alpha glucosidase II, alpha 135 - gi|62641851 5 9 4 7 63 213 3.07 8.13 subunit 136 similar to alpha-2u-globulin - gi|62649094 3 137 137 similar to alpha-3 type IV collagen - gi|62655284 5 2.07 138 similar to AP47 protein - gi|62662374 3 67 139 similar to APC2 protein - gi|62651748 2 1.70 140 similar to apoptosis inhibitor 5 - gi|62645438 2 1.40 similar to ARP2/3 complex 21 kDa 141 subunit (p21-ARC) (Actin-related - gi|27665454 2 69 protein 2/3 complex subunit 3) similar to ATPase, Class VI, type 11C 142 - gi|62667482 2 1 79 2.00 isoform a 143 similar to ATPase, H+ transporting, V1 - gi|34869154 6 7 200 8.53 subunit A, isoform 1 similar to ATP-binding cassette 144 - gi|62657287 4 4 187 8.00 transporter sub-family A member 6 similar to ATP-binding cassette 145 - gi|62657283 2 44 transporter sub-family A member 8a similar to ATP-binding cassette, 146 - gi|62660110 2 2.23 subfamily G, member 3 147 similar to BC049975 protein - gi|62651460 5 111 similar to brain-specific angiogenesis 148 - gi|62649735 5 3 1.42 1.31 inhibitor 2 149 similar to calmin delta - gi|62651197 2 1.40 150 similar to Carboxylesterase 2 - gi|62642570 3 59 similar to Carboxypeptidase N 83 kDa chain precursor (Carboxypeptidase N 151 - gi|62658037 2 2 2.00 1.70 regulatory subunit) (Carboxypeptidase N polypeptide 2) Similar to choline phosphotransferase 152 1; cholinephosphotransferase 1 alpha; Q66H21 gi|56090323 2 1 55 2.00 cholinephosphotransferase 1 153 similar to collagen type XVII - gi|62642454 1 1.70 similar to C-type lectin superfamily 4, 154 - gi|62658365 1 1.70 member G 155 similar to cytochrome P450 2B15 - gi|62639273 2 87 156 similar to desmoglein 2 - gi|62664095 1 55 similar to Disco-interacting protein 2 157 - gi|62665845 11 8 10 7 50 50 2.05 2.10 homolog similar to DnaJ homolog subfamily C 158 - gi|62654214 5 9 7 53 2.04 2.02 member 13 159 similar to early quiescence protein-1 - gi|27677818 1 2 61 2.00 similar to eukaryotic translation 160 - gi|62642556 7 5 13 9 74 74 4.02 3.73 initiation factor 3, subunit 10 theta similar to FERM, RhoGEF and 161 - gi|62655415 2 44 pleckstrin domain protein 2 similar to G protein-coupled receptor 162 - gi|62643936 2 48 89 163 similar to glucuronosyltransferase I - gi|34861582 3 6 106 6.04 similar to glutaminyl-peptide 164 - gi|62639259 3 56 cyclotransferase-like similar to Glutathione S-transferase, 165 - gi|62665863 5 7 254 11.40 theta 3 166 similar to GPI7 - gi|62660028 6 7 117 5.18 similar to GRP1 binding protein 167 - gi|62647869 8 1.40 GRSP1 168 similar to heat shock protein 1, beta - gi|62666933 4 61 169 similar to heat shock protein 8 - gi|62642467 2 5 89 1.70 170 similar to heat shock protein 8 - gi|62644475 2 51 similar to hexose-6-phosphate 171 dehydrogenase (glucose 1- - gi|62650056 6 2 4 2 41 75 2.00 3.70 dehydrogenase) similar to ilvB (bacterial acetolactate 172 - gi|34862359 4 5 192 6.00 synthase)-like 173 Similar to interferon-inducible GTPase Q5FVQ6 gi|58477737 1 2 53 2.00 similar to lipoprotein receptor-related 174 - gi|62652278 19 23 18 33 24 40 418 459 28.66 28.53 protein similar to M6PR domain containing 175 - gi|62655863 1 43 protein 1 precursor similar to macrophage mannose 176 - gi|62663924 6 8 11 12 81 171 5.42 11.57 receptor precursor similar to major facilitator superfamily 177 - gi|62643542 1 2.00 domain containing 1 similar to mannosidase, alpha, class 178 - gi|62640781 3 4 63 2.01 2A, member 2 179 similar to matriptase-2 - gi|62652706 4 2.18 similar to Microsomal glutathione S- 180 transferase 2 (Microsomal GST-2) - gi|27690924 1 1 77 2.00 (Microsomal GST-II) 181 similar to mKIAA1631 protein - gi|62644141 2 5 4 4 66 66 2.00 1.31 similar to N- 182 - gi|62656023 2 3 1 3 43 73 1.70 2.02 acetylglucosaminyltrasnferase IVb 183 similar to Nodal modulator 1 - gi|34856103 1 2.00 similar to peptidoglycan recognition 184 - gi|62651804 6 67 protein 2 185 similar to peptidylprolyl isomerase A - gi|62655214 2 45 186 similar to periplakin - gi|62655692 6 47 similar to peroxisomal biogenesis 187 - gi|62660884 1 1.30 factor 13 similar to Poly(rC)-binding protein 1 188 - gi|62647735 3 4 5 56 156 9.30 (Alpha-CP1) (hnRNP-E1) similar to pregnancy-associated plasma 189 - gi|62649105 2 44 protein-A 190 similar to Protein HSPC163 - gi|27679416 1 1 2 1 103 103 2.00 2.00 similar to protein phosphatase 1 191 - gi|34857062 5 5 111 5.54 (formerly 2C)-like 192 similar to PU.1 binding protein Pub - gi|62649066 4 4 7 4 52 52 2.01 1.31 193 similar to RanBp21 - gi|62654712 5 6 69 4.22 194 similar to RHOD - gi|27661195 1 1 3 2 83 83 2.00 2.00 similar to Rho-related GTP-binding 195 - gi|27660254 2 3 45 70 protein RhoC similar to Ribosome-binding protein 1 196 - gi|62645952 4 5 76 1.39 (Ribosome receptor protein) (mRRp) 197 similar to RNA helicase - gi|62666532 5 7 56 4.02 similar to scavenger receptor type A 198 - gi|62662711 3 54 SR-A 199 similar to serine/threonine kinase - gi|62659973 4 3 54 2.00 similar to serologically defined breast 200 - gi|626462082264 7445457979 6.005.00 cancer antigen 84 isoform a 201 similar to Snx5 protein - gi|62645955 1 2.00 similar to solute carrier family 30 (zinc 202 - gi|62650354 1 3 51 2.21 transporter), member 6 similar to solute carrier family 35, 203 - gi|62650165 1 1 43 2.00 member E2 204 similar to spermatogenesis associated 5 - gi|62643360 2 53 similar to SPFH domain family, 205 - gi|34879021 2 2 3 50 50 2.00 member 2 similar to SPFH domain family, 206 - gi|62642357 4 3 50 2.04 member 2 similar to squamous cell carcinoma 207 - gi|62666043 2 59 antigen recognized by T cells 2 208 similar to t-complex protein 10b - gi|62638559 6 1.31 similar to tetratricopeptide repeat 209 - gi|34867701 3 46 domain 3 similar to thyroid hormone receptor 210 - gi|62651158 22 22 504 22.70 interactor 11 211 similar to Zinc finger protein 406 - gi|62652546 2 1.80 212 similar to zinc finger protein 69 - gi|62639437 2 49 213 similar to zinc transporter 5 - gi|62642842 2 2 4 63 105 4.00 214 SLC10A5 Q4JLT5 gi|70608094 2 3 95 2.92 Solute carrier family 27 (Fatty acid 215 Q66HN6 gi|3087820 3 44 transporter), member 32 216 Synaptosomal-associated protein 29 Q9Z2P6 gi|6685966 2 3 5 3 105 131 4.01 6.00 217 TATA element modulatory factor Q9QYA5 gi|6650548 10 10 9 12 233 336 10.08 13.06 T-cell, immune regulator 1, ATPase, 218 H+ transporting, lysosomal V0 protein - gi|62641689 1 2.00 a isoform 3 219 TORID Q925D4 gi|37590771 2 2 75 2.00 transforming growth factor, beta 220 - gi|62663187 5 2.00 induced, 68 kDa (predicetd) 221 Transketolase P50137 gi|1729977 4 4 4 3 103 107 4.80 3.34 Transmembrane 9 superfamily protein 222 Q4KLL4 gi|68533829 9 12 9 14 9 12 9 13 371 423 463 605 14.10 14.61 12.93 18.78 member 4 223 Ubiquitin specific protease 19 Q6J1Y9 gi|47525210 9 3 2.03 1.31 224 Ubiquitin-like protein FAT10 Q921A3 gi|46237703 1 33 UDP glycosyltransferase 1 family 225 Q6T5F3 gi|40849836 4 177 polypeptide A11 UDP glycosyltransferase 1 family 226 Q6T5F1 gi|40849840 5 2.01 polypeptide A4 UDP glycosyltransferase 1 family 227 Q6T5E9 gi|40849844 4 177 polypeptide A7 UDP glycosyltransferase 1 family 228 Q6T5E7 gi|40849848 4 177 polypeptide A9 UDP glycosyltransferase 2 family, 229 Q5EBC8 gi|59809138 8 290 polypeptide B 230 UDP-glucuronate decarboxylase Q8K464 gi|21326465 3 4 113 4.43 231 UDP-glucuronosyltransferase 1A5 Q8VD45 gi|18308168 5 229 232 UDP-glucuronosyltransferase 1A6 P97886 gi|1890306 5 5 242 6.09 Vacuolar ATP synthase subunit B, 233 P62815 gi|74213615 2 3 54 54 brain isoform

Microsomal 3-oxo-5-alpha-steroid 4-dehydrogenase 1 P24008 gi|206838 2 1 44 44 1 2 Carboxylesterase isoenzyme Q8K3R0 gi|21426807 6 7 158 7.55 Cytochrome P450, family 2, subfamily 3 Q6AZ78 gi|50925431 3 61 d, polypeptide 9 Dimethylaniline monooxygenase [N- 4 P36365 gi|78099773 4 2 3.41 2.89 oxide-forming] 1 Dimethylaniline monooxygenase [N- 5 Q9EQ76 gi|78099259 5 4 6 2 4 7 78 74 186 2.09 4.00 9.24 oxide-forming] 3 Dimethylaniline monooxygenase [N- 6 Q8K4C0gi|213115186364 776564135153 6.985.40 oxide-forming] 5 7 Epoxide hydrolase 1 P07687 gi|38181831 10 10 12 11 8 7 14 11 231 184 194 170 10.07 8.43 14.46 12.70 8L-gulonolactone oxidase P10867gi|1211415687538673672121871.421.3211.0410.85 9 Long-chain-fatty-acid--CoA ligase 1 P18163 gi|126011 17 16 18 18 17 14 19 18 390 323 726 690 15.36 11.98 29.21 26.47 10Long-chain-fatty-acid--CoA ligase 5 O88813gi|60164843344 8510180217193 6.636.56 11 Long-chain-fatty-acid--CoA ligase 6 P33124 gi|73970627 3 82 Membrane associated progesterone 12 P70580gi|3127857454443551741661871916.004.596.966.50 receptor component 1 13Microsomal glutathione S-transferase 1P08011gi|38649092325422641691524453922.012.018.008.00 Prostaglandin G/H synthase 1 14 Q63921 gi|3914292 1 32 [Precursor] 15 Retinol dehydrogenase 7 P55006 gi|68534258 5 4 4 9 4 44 127 103 8.02 7.30 16 Retinol dehydrogenase type II P50170 gi|1710630 4 4 4 7 41 106 1.99 4.00 similar to Putative dimethylaniline 17 - gi|34880876 2 2 74 87 monooxygenase [N-oxide-forming] 6 Stress 70 protein chaperone 18 microsome-associated 60 kDa protein O35162 gi|67461586 3 2 47 47 [Precursor] UDP-glucuronosyltransferase 1-1 19 Q64550 gi|2501473 7 7 6 7 7 33 247 216 6.09 3.72 precursor, microsomal UDP-glucuronosyltransferase 1-2 20 P20720 gi|207579 6 4 201 196 precursor, microsomal UDP-glucuronosyltransferase 1-5 21 Q64638 gi|2501477 5 6 201 2.01 precursor, microsomal UDP-glucuronosyltransferase 1-6 22 P08430 gi|136726 5 4 239 4.00 precursor, microsomal UDP-glucuronosyltransferase 1-8 23 Q64634 gi|2501482 4 161 precursor, microsomal UDP-glucuronosyltransferase 2B1 24 P09875 gi|136728 4 3 3 3 187 168 2.04 2.01 [Precursor] UDP-glucuronosyltransferase 2B12 25 P36511 gi|549157 5 5 8 7 222 190 6.97 5.94 [Precursor] UDP-glucuronosyltransferase 2B15 P54855 26 gi|458399 2 5 132 6.20 [Precursor] human UDP-glucuronosyltransferase 2B2 27 P08541 gi|207583 4 9 8 4 10 8 35 331 290 1.53 6.01 6.01 [Precursor] UDP-glucuronosyltransferase 2B3 28 P08542 gi|57449 5 7 8 9 9 34 369 329 12.96 12.28 [Precursor] UDP-glucuronosyltransferase 2B6 29 P19488 gi|136733 8 8 9 8 276 253 4.00 3.70 [Precursor] UDP-glucuronosyltransferase 2B8 30 Q62789 gi|1177818 2 2 167 50 [Precursor]

Membrane assosiated 1 3-keto-steroid reductase Q62904 gi|8134405 2 3 2 33 2.00 1.70 2 ABC transporter ABCG3 Q68HW7 gi|51243003 2 45 3 Acetyl-CoA carboxylase O70151 gi|3080546 7 32 4 Aminopeptidase N P15684 gi|601865 4 3 3 2 115 110 2.11 1.33 5 Amyloid-like protein 2 [Precursor] P15943 gi|1703345 5 2 36 1.40 6 Anion exchange protein 2 P23347 gi|114792 3 1 5 1 63 63 2.00 2.00 7 ATPase 7B [Fragment] Q9R0T2 gi|6006291 2 67 ATP-binding cassette sub-family G 8 P58428 gi|38258880 1 36 member 8 9 Bile salt export pump O70127 gi|12585136 2 11 10 8 7 38 165 162 9.05 8.56 10 Brain acid soluble protein 1 Q05175 gi|730110 1 1 2 2 68 68 2.00 2.00 cAMP-dependent protein kinase type 11 P12368 gi|125201 4 4 4 2 64 64 3.40 3.70 II-alpha regulatory subunit [Fragment] Canalicular multispecific organic anion 12 Q63120 gi|1405353 5 3 5 3 74 74 1.98 1.53 transporter 1 13 Carboxypeptidase D [Precursor] Q9JHW1 gi|62510319 9 9 12 10 13 12 75 56 426 382 22.01 21.01 14 Catechol O-methyltransferase P22734 gi|116909 3 3 5 3 121 120 6.00 6.00 15 Cationic amino acid transporter-2 Q4PLF2 gi|67942063 3 1 47 1.30 16 Cc1-3 Q7TP16 gi|62990119 5 3 58 2.00 clone:M5C1109K17 product:discs, Q3UGX5 17 gi|74188686 9 37 large homolog 5 (Drosophila) mouse Core1 UDP-galactose:N- 18 acetylgalactosamine-alpha-R beta 1,3- Q9JJ05 gi|8927166 5 4 111 5.23 galactosyltransferase 19Cytochrome b5 P00173gi|562697685599551094353695033946.596.2414.1314.10 Q9JJ02 gi|8886066 20 Cytochrome P450 CYP2B21 299 P00176 gi|117206 21 Cytochrome P450, 4a10 Q642E9 gi|27819673 3 79 22 Delta-5 fatty acid desaturase Q920R3 gi|15823618 3 3.70 DnaJ (Hsp40) homolog, subfamily A, 23 Q4QR73 gi|67677946 1 40 member 4 24 DnaJ homolog subfamily A member 1 P63036 gi|51702257 2 40 Down syndrome cell adhesion 25 Q8VHZ8 gi|18033454 2 61 molecule DSCAM Ectonucleotide 26 P97675 gi|66911975 3 2 45 45 pyrophosphatase/phosphodiesterase 3 27 Endothelin-converting enzyme 1 P42893 gi|1706564 7 4 8 4 81 69 4.02 4.00 28 Estradiol 17-beta-dehydrogenase 2 Q62730 gi|3334165 4 4 3 1 53 53 2.01 2.00 Ezrin-radixin-moesin binding 29 Q9JJ19 gi|41688553 3 2 3 3 91 88 2.96 1.79 phosphoprotein 50 30 Fatty acid synthase P12785 gi|2506136 12 9 9 8 75 79 2.17 1.41 31 Glucose transporter type 2 [Fragment] Q6LE97 gi|535736 1 57 32 Glutamyl aminopeptidase P50123 gi|7673021 8 1.42 33 Glycoprotein 38 [Precursor] Q64294 gi|2498421 1 53 Guanine nucleotide-binding protein, 34 Q63210 gi|6016101 3 3 2.01 1.71 alpha-12 subunit 35 HIG1 domain family member 1A Q8VH49 gi|76363184 1 2.00 36 Insulin receptor [Precursor] P15127 gi|124531 9 1.42 37 Integrin beta-1 [Precursor] P49134 gi|1352494 3 3 7 2 63 63 2.02 2.01 38 Interferon-inducible protein P26376 gi|124492 1 1 1 1 115 113 2.00 2.00 Interleukin-6 receptor beta chain 39 P40190 gi|729835 6 32 [Precursor] 40 JTB protein [Precursor] O88823 gi|38304026 3 2 2 1 118 109 2.00 2.00 41 L-gulonolactone oxidase Q5EBC1 gi|59808907 6 96 42 Liver-specific transport protein Q63314 gi|529590 1 56 Long-chain fatty acid transport protein 43 P97849gi|18817135464 6548489891 4.024.01 1 L-type calcium channel alpha-1c 44 Q8VHT2 gi|17864840 10 33 subunit 45 MAL2A Q7TPB7 gi|32693285 1 1 69 2.00 46 Multidrug resistance protein 1a Q9JK64 gi|7739773 8 36 Multidrug resistance-associated protein 47 Q9QYM0 gi|11133307 7 1.42 5 Myeloid-associated differentiation 48 Q6VBQ5 gi|33590376 1 58 marker 49 Na-K-Cl cotransporter Q9QX10 gi|13929130 4 1.71 50 olfactory receptor Olr170 - gi|47576697 2 1 1.70 2.00 51 Oncostatin M specific receptor Q65Z14 gi|52000489 1 1.30 Orphan sodium- and chloride- 52 dependent neurotransmitter transporter Q08469 gi|730198 1 36 NTT73 53 Perforin 1 [Precursor] P35763 gi|548477 1 2.00 54 P-glycoprotein sister O88331 gi|3273484 4 75 Phosphatidylethanolamine-binding 55 P31044 gi|406294 1 1 1 1 68 68 2.00 2.00 protein 56 Phospholemman [Precursor] O08589 gi|1916012 1 1 49 50 Pleckstrin homology domain- Q9QZC7 57 gi|48474680 1 36 containing protein family B member 2 mouse Potassium-transporting ATPase alpha 58 P09626 gi|203037 4 3 2 44 44 2.00 chain 1 Potassium-transporting ATPase alpha 59 P54708 gi|1703464 4 3 3 34 44 44 chain 2 Probable phospholipid-transporting Q8TF62 60 gi|30315933 3 1.40 ATPase IM human Pro-neuregulin-2, membrane-bound 61 O35569 gi|3914152 7 1.32 isoform [Precursor] Proteasome (Prosome, macropain) 26S 62 Q6P7R9 gi|81911306 5 2.01 subunit, ATPase 2 Q8BUV8 63 Protein GPR107 [Precursor] gi|71152087 2 3 2 94 2.00 2.01 mouse 64Ras-related protein Rap-1A P62836gi|537335732233 434848141114 6.006.00 Receptor tyrosine-protein kinase erbB- 65 Q62799 gi|21431758 6 33 3 [Precursor] 66 RT1 class I, A2 Q6MGB8 gi|46237547 3 2 67 67 67 Serum paraoxonase/arylesterase 2 Q6AXM8 gi|71153065 3 2 1 1 44 44 2.00 1.70 similar to chromosome 5 open reading 68 - gi|34870715 4 3 1 3 4 61 111 2.00 2.89 5.77 frame 15 similar to growth arrest-specific protein 69 - gi|62639812 4 3 46 44 2 70 similar to meltrin alpha - gi|62641531 7 1 2.00 1.70 71 similar to PL6 protein - gi|34865897 4 2 2 4 115 117 4.00 4.01 similar to transmembrane protein 72 - gi|34862730101087989733223715912313.2011.559.018.90 TM9SF3 similar to zinc finger, DHHC domain 73 - gi|62639789 4 4 62 62 containing 13 74 Slc30a7_predicted protein [Fragment] Q5BJM8 gi|60688531 3 2 2 51 61 4.00 75 Sodium/bile acid cotransporter P26435 gi|127792 1 1 3 1 87 87 2.00 2.00 Sodium/potassium-transporting 76 P06685 gi|38303881 9 8 8 7 236 228 12.31 11.70 ATPase alpha-1 chain [Precursor] Sodium/potassium-transporting 77 Q64541 gi|18202605 3 2 44 44 ATPase alpha-4 chain Solute carrier family 4 sodium 78 bicarbonate cotransporter-like member Q6PU72 gi|46361421 3 55 10 rb5NCBE 79 Sterol 12-alpha hydroxylase Q9WTN7 gi|4587057 4 77 80 Sulfate anion transporter 1 P45380 gi|1173364 2 1 2.00 2.00 81 Synaptic glycoprotein SC2 Q64232 gi|37589607 2 2 2 3 2 71 71 1.40 2.55 2.23 82 Transforming protein RhoA P61589 gi|47605935 1 3 1 1 1 45 71 1.70 2.00 2.00 Transmembrane 7 superfamily member 83 Q5BK21 gi|60551458 1 1 60 2.00 2 Transmembrane 9 superfamily protein 84 Q66HF2gi|622875469998961081601354174093.102.6116.0015.00 member 1 [Precursor] Type I transmembrane C-type lectin 85 Q5FVR3 gi|58476453 1 1 63 2.00 receptor DCL-1 Voltage-dependent R-type calcium 86 Q07652 gi|1705707 3 3 1.31 channel alpha-1E subunit Zinc finger DHHC domain containing 87 Q923G5 gi|28202092 2 1 1 35 1.40 1.30 protein 7 Q9DB43 88 Zinc finger protein-like 1 gi|61251931 3 2 4 5 3 45 41 44 4.36 3.77 mouse

Cytoplasmic 10-formyltetrahydrofolate 1 P28037 gi|1346044 3 2 7 4 97 97 3.41 3.31 dehydrogenase 2 14-3-3 protein zeta/delta P63102 gi|52000883 2 2.00 3 26S protease regulatory subunit 6B Q63570 gi|2492517 2 39 4 3-alpha-hydroxysteroid dehydrogenase P23457 gi|60688159 4 3 4 4 75 78 4.36 3.50 5 40S ribosomal protein S10 P63326 gi|54039307 2 1 1 35 2.00 2.00 6 40S ribosomal protein S14 P13471 gi|133785 4 3 3 2 93 82 4.00 4.00 7 40S ribosomal protein S15 P62845 gi|51338619 2 1 1 41 2.00 1.70 8 40S ribosomal protein S15a P62246 gi|54039450 3 3 3 64 64 2.04 9 40S ribosomal protein S16 P62250 gi|54039370 3 1 2 2 2 3 71 61 61 2.00 2.00 2.01 10 40S ribosomal protein S17 P04644 gi|54041951 1 2 2 51 51 2.00 11 40S ribosomal protein S18 P62271 gi|50403620 3 33 12 40S ribosomal protein S19 P17074 gi|133857 2 3 4 33 2.36 1.53 1340S ribosomal protein S2 P27952gi|1339141269 5 369267169 4.01 14 40S ribosomal protein S20 P60868 gi|46397701 2 2 4 3 50 50 2.01 2.01 15 40S ribosomal protein S26 P62856 gi|51338622 3 2 2 2 91 91 2.00 2.01 16 40S ribosomal protein S3 P62909 gi|51703302 4 4 5 5 138 127 6.36 5.86 17 40S ribosomal protein S30 P62864 gi|1334234 1 1 1 1 49 49 2.00 2.00 18 40S ribosomal protein S4, X isoform P62703 gi|50403621 3 35 19 40S ribosomal protein S7 P62083 gi|49065830 3 35 20 40S ribosomal protein S8 P62243 gi|54039527 2 3 3 3 101 90 3.40 2.49 21 40S ribosomal protein S9 P29314 gi|52788199 2 3 5 2 36 49 3.00 1.36 22 40S ribosomal protein SA P38983 gi|730681 1 4 5 4 4 35 104 110 5.40 4.86 4-trimethylaminobutyraldehyde 23 Q9JLJ3 gi|7248632 4 3 3 3 125 111 4.57 4.49 dehydrogenase 24 60S acidic ribosomal protein P0 P19945 gi|57708 2 3 3 2 88 84 2.00 2.00 25 60S ribosomal protein L11 P62914 gi|51702792 3 2 3 2 102 97 4.00 3.00 26 60S ribosomal protein L13 P41123 gi|730529 1 2 1 1 44 44 2.00 2.00 27 60S ribosomal protein L18 P12001 gi|54261673 2 2 6 2 131 121 4.01 4.00 28 60S ribosomal protein L18a P62718 gi|50403587 2 2 1 2 57 57 2.00 1.70 29 60S ribosomal protein L21 P20280 gi|132775 1 2 6 3 47 47 2.00 2.01 30 60S ribosomal protein L24 P83732 gi|41019239 3 3 5 2 68 68 4.01 3.70 31 60S ribosomal protein L32 P62912 gi|51702804 1 2.00 32 60S ribosomal protein L4 P50878 gi|1710511 4 3 63 61 33 60S ribosomal protein L8 P62919 gi|3851579 1 1 3 3 62 62 2.00 2.00 Abnormal spindle-like microcephaly- P62290, 34 gi|60391787 15 34 associated protein homolog Gibbon 35 Acetyl-CoA carboxylase 1 P11497 gi|116670 10 5 45 45 36 Actin, alpha skeletal muscle P68136 gi|61217738 5 314 P60711 gi|46397316 37 Actin, cytoplasmic 1, cytoplasmic 2 11 12 10 11 10 10 9 10 271 202 693 530 10.67 8.64 15.62 14.20 P63259 gi|54036665 P62738 gi|51316969 Actin: aortic smooth muscle, alpha P68035 gi|54036667 38 cardiac, gamma-enteric smooth muscle, 56 6 381314 2.00 P63269 gi|54036666 alpha skeletal muscle P68136 gi|61217738 39 Actn4 protein Q6P786 gi|38197444 2 2 11 7 7 3 42 42 158 151 6.05 6.00 40 Adenosylhomocysteinase P10760 gi|134185 7 5 5 5 109 108 2.26 1.77 41 Alcohol dehydrogenase A chain P06757 gi|202727 3 2 5 66 64 1.40 Aldehyde dehydrogenase, dimeric 42 P11883 gi|118507 4 3 52 52 NADP-preferring 43 Alpha-actinin 1 Q9Z1P2 gi|13123942 6 3 70 70 44 Alpha-enolase P04764 gi|38649320 3 3 6 3 80 71 4.00 3.70 45 Annexin A6 P48037 gi|763181 6 7 6 9 6 44 170 142 7.70 6.95 46 Apoptotic death agonist BID Q9JLT6 gi|7381175 1 45 47 Arginase-1 P07824 gi|60551387 4 6 7 5 188 171 6.05 6.46 48 Arsenite methyltransferase Q8VHT6 gi|57012546 4 4 3 3 67 66 3.70 4.00 Aspartate aminotransferase, 49 P13221 gi|112978 2 34 cytoplasmic 50 beta actin - gi|71620 9 312 51 Beta-catenin Q9WU82 gi|9972860 4 3 4 3 51 51 2.00 1.71 Betaine--homocysteine S- 52 O09171 gi|3913156 4 4 12 12 3 14 13 75 53 342 347 2.02 17.11 19.78 methyltransferase 53 Beta-ureidopropionase Q03248 gi|416730 3 3 2 1 56 56 2.00 2.00 Bullous pemphigoid antigen 1, Q91ZU6 54 gi|30315937 20 34 isoforms 1/2/3/4 mouse 55 Calmodulin P62161 gi|49037408 2 4 2 2 105 97 4.00 4.00 cAMP-dependent protein kinase, beta- 56 P68182 gi|59799765 1 3 2 50 2.00 2.00 catalytic subunit Capping protein (Actin filament) 57 Q3T1K5 gi|74355722 2 66 muscle Z-line, alpha 2 58 Carbonic anhydrase 3 P14141 gi|203225 4 3 5 4 53 52 3.95 2.78 59 Casein kinase I, gamma 1 isoform Q62761 gi|50925493 6 6 190 8.00 60 Catechol O-methyltransferase P22734 gi|116909 3 3 5 3 121 120 6.00 6.00 Catenin (Cadherin-associated protein), 61 Q5U302 gi|55249717 8 7 7 5 51 51 4.01 4.09 alpha 1, 102kDa clone:D930020A05 product:Ras Q3UQ44 62 GTPase-activating-like protein gi|74218637 7 7 14 6 97 133 2.35 4.50 mouse IQGAP2 homolog [Fragment] 63 Cystathionine beta-synthase P32232 gi|543960 4 2 2.00 2.00 64 Cystathionine gamma-lyase P18757 gi|1705789 3 8 6 8 6 34 251 235 10.01 8.16 Q62167 65 DEAD-box protein 3, X-chromosomal gi|2500528 6 11 70 4.03 mouse 66 DEAD-box protein 3, Y-chromosomal Q62095 gi|55562828 2 48 67 DnaJ homolog subfamily C member 3 Q9R0T3 gi|73620810 3 3 6 3 101 97 2.31 2.01 68Elongation factor 1-alpha 1 P62630gi|5040209533222 4360531021021.40 2.042.03 Eukaryotic translation initiation factor 69 P68101 gi|61226304 5 3 3 1 69 69 2.00 2.00 2 subunit 1 Eukaryotic translation initiation factor 70 Q6P3V8 gi|39793992 9 7 9 5 129 151 6.33 5.80 4A, isoform 1 Eukaryotic translation initiation factor 71 Q5RKI1 gi|55716055 6 116 4A2 Ezrin-radixin-moesin binding 72 Q9JJ19 gi|41688553 3 2 3 3 91 88 2.96 1.79 phosphoprotein 50 73 Fatty acid-binding protein, brain P55051 gi|1706751 1 1 6 2 53 53 2.01 2.00 74 Fatty acid-binding protein, liver P02692 gi|119810 1 1 4 44 44 2.00 75 Galpha13 Q6Q7Y5 gi|71089933 3 1 56 56 76 Gamma-enolase P07323 gi|37805239 3 3 52 52 77 Glutathione peroxidase 1 P04041 gi|2654236 2 2 5 4 73 85 5.71 5.40 Glutathione S-transferase alpha 1 P00502 gi|62822551 78 343 354747 Glutathione S-transferase alpha 2 P04903 gi|121713 79 Glutathione S-transferase alpha 3 P04904 gi|1170084 2 3 3 2 4 36 58 46 2.01 2.58 80 Glutathione S-transferase alpha 5 P46418 gi|1170085 2 1 39 1.30 81 Glutathione S-transferase Mu 1 P04905 gi|38648907 6 7 5 166 146 8.54 82 Glutathione S-transferase Mu 2 P08010 gi|121719 3 3 3 5 7 67 149 135 6.01 10.17 83 Glutathione S-transferase theta 2 P30713 gi|1170118 1 1 2 65 65 2.00 84 Glutathione S-transferase Yb-3 P08009 gi|121721 3 3 4 67 162 77 Glyceraldehyde-3-phosphate 85 P04797 gi|120707 3 4 5 5 107 97 7.40 6.15 dehydrogenase 86 Heat shock 90kDa protein 1, beta Q66H55 gi|51859516 6 9 296 11.85 87 Heat shock cognate 71 kDa protein P63018 gi|51702273 8 9 14 13 7 6 15 16 202 159 691 649 6.73 5.72 26.01 25.31 88 Heat shock protein 86 Q91XW0 gi|54673763 3 8 12 7 6 37 208 353 4.00 4.00 89 Heat shock protein 90 Q68GV5 gi|51243733 12 389 90 Heat shock protein HSP 90-beta P34058 gi|1346320 5 12 5 12 35 389 66 12.53 Heterogeneous nuclear 91 P61980 gi|48429097 3 3 3 1 85 85 2.01 2.00 ribonucleoprotein K 92 Hsp90 co-chaperone Cdc37 Q63692 gi|32172404 2 3 2 37 1.40 1.31 93 Hypothetical protein Q4FZU2 gi|71051822 2 3 79 84 94 Hypothetical protein MGC108896 Q5BK56 gi|60552114 4 147 Hypothetical protein 95 Q4QQV0 gi|67678286 5 5 188 171 RGD1305887_predicted 96 Integrin-linked kinase ILK Q99J82 gi|1311165 3 1 2 2 64 64 2.00 2.00 97 Inter-alpha-inhibitor H4 heavy chain Q5EBC0 gi|59808174 5 11 4 14 59 468 3.78 20.48 P24712 98 Involucrin gi|124737 3 41 tamarin Isocitrate dehydrogenase [NADP] 99 P41562 gi|1170478 3 2 5 3 67 67 2.00 2.00 cytoplasmic 100 Junction plakoglobin Q6P0K8 gi|41350891 3 3 6 79 79 2.00 101 Keratin, type II cytoskeletal 1b Q6IG01 gi|46485120 5 5 70 70 102 Keratin, type II cytoskeletal 5 Q6P6Q2 gi|33519156 2 75 Q61097 103 Kinase suppressor of ras-1 gi|56748938 5 35 mouse 104 L-lactate dehydrogenase A chain P04642 gi|126051 5 4 4 3 81 75 3.44 1.80 L-serine dehydratase/L-threonine 105 P09367 gi|134387 3 2 1 34 2.00 2.00 deaminase Q9WVL0 106 Maleylacetoacetate isomerase gi|11133639 3 1.44 mouse 107 Moesin O35763 gi|32363196 3 2 52 52 Q8CI43 108 Myosin light chain 1 slow a gi|81878172 2 61 mouse 109 Myosin light polypeptide 6 Q64119 gi|2842665 2 2 3 2 95 83 3.70 2.85 110 Myosin-10 Q9JLT0 gi|13431672 8 40 Q8IUG5 111 Myosin-18B gi|32699565 11 34 human Q64331 112 Myosin-6 gi|13431710 10 9 37 2.02 mouse 113 Myosin-9 Q62812 gi|13431671 16 8 15 4 103 117 5.44 3.07 Nascent polypeptide-associated P70670 114 complex alpha subunit, muscle-specific gi|71151989 7 35 mouse form 115 Nucleobindin 2 [Precursor] Q9JI85 gi|14549433 12 12 20 18 10 9 14 15 458 396 1070 874 12.64 12.68 24.40 23.61 116 Nucleoside diphosphate kinase A Q05982 gi|462690 3 2 2 61 61 2.00 117 Nucleoside diphosphate kinase B P19804 gi|127984 2 3 61 2.00 118 PDZ and LIM domain protein 1 P52944 gi|1020151 2 1 3 1 45 45 1.70 1.72 119 PDZ domain containing protein 1 Q9JJ40 gi|73621376 4 2 2.05 1.31 120 Peptidyl-prolyl cis-trans isomerase A P10111 gi|118107 2 2 3 3 45 45 2.96 2.89 121 Peroxiredoxin 1 Q63716 gi|56789700 4 4 6 4 132 131 6.01 6.00 Phosphatidylethanolamine-binding 122 P31044 gi|406294 1 1 1 1 68 68 2.00 2.00 protein 123 Phosphatidylinositol 4-kinase beta O08561 gi|38372399 4 41 Phosphoenolpyruvate carboxykinase, 124 P07379 gi|130757 5 3 50 50 cytosolic [GTP] 125 Phosphoglycerate kinase 1 Q5M945 gi|56585024 4 3 3 48 48 2.00 126 Phosphoglycerate kinase 2 Q5XIV1 gi|54035400 2 2 2 48 48 2.00 127 Plakoglobin P70565 gi|1497985 3 4 123 3.30 128 Polyadenylate-binding protein 1 Q9EPH8 gi|47605941 5 4 7 7 66 54 2.97 2.87 129 Polyubiquitin Q63429 gi|471154 2 5 82 179 130 Profilin-1 P62963 gi|1628436 3 2 4 2 77 70 4.00 3.30 Proteasome (Prosome, macropain) 131 Q6PDW4 gi|37231712 2 1 2.00 1.30 subunit, beta type 1 132 Proteasome subunit alpha type 1 P18420 gi|130849 3 3 66 66 133 Proteasome subunit alpha type 4 P21670 gi|130862 4 33 134 Proteasome subunit alpha type 5 P34064 gi|286254 2 1 2 1 57 57 2.00 2.00 Proteasome, 26S, non-ATPase 135 Q6PCT9 gi|37748489 5 3 67 67 regulatory subunit 6 136 Radixin Q5WQV5 gi|40804379 3 3 7 6 68 64 5.71 4.49 137 Regucalcin Q03336 gi|408807 2 2 4 3 84 74 2.12 2.03 Ribonucleoside-diphosphate reductase 138 Q4KLN6 gi|77416595 4 37 M2 subunit 139 Ribosomal protein L28 Q642E2 gi|51980292 1 2 1 2 47 47 2.00 2.00 140 Ribosomal protein S27a Q6PED0 gi|37194821 5 5 177 6.02 141 Rps12 protein Q6PDW1 gi|34849622 2 3 2 43 43 1.40 142 Rps16 protein [Fragment] Q6P3E1 gi|51702822 2 3 58 1.70 143 similar to 60S ribosomal protein L11 - gi|62650100 3 82 144 similar to Apolipoprotein C2 - gi|27676424 1 1.70 similar to dual-specificity Rho- and 145 - gi|62664285 6 2.02 Arf-GTPase activating protein 1 146 similar to keratin Kb40 - gi|62653092 3 94 147 similar to myosin-VIIb - gi|62664168 12 523 similar to RIKEN cDNA 4732495G21 148 - gi|27687455 7 211 gene Staphylococcal nuclease domain 149 Q66X93 gi|60415342 7 39 containing protein 1 150 Sterol carrier protein 2 Q642G0 gi|51980631 3 3 3 2 50 50 2.00 1.31 Structural maintenance of chromosome Q8CG48 151 gi|30173243 9 34 2-like 1 protein mouse 152 Sulfotransferase 1A1 P17988 gi|135009 2 1 36 2.00 Sulfotransferase family cytosolic 1B 153 P52847 gi|3915863 2 2 3 3 139 121 4.11 4.03 member 1 154Superoxide dismutase [Cu-Zn] P07632gi|207012434433341351162702554.003.706.006.01 P26039 155 Talin-1 gi|135290 9 35 mouse 156 T-complex protein 1, alpha subunit P28480 gi|135539 3 1 4 4 72 72 1.71 2.01 157 Trap1 protein Q5XHZ0 gi|54035509 7 5 80 80 158 Tubb3 protein Q4QRB4 gi|67677915 6 7 251 229 159 Tubulin alpha-1 chain P68370 gi|38328248 6 239 160 Tubulin alpha-2 chain Q6P9V9 gi|55976173 6 6 269 243 161 Tubulin alpha-6 chain Q6AYZ1 gi|50927313 6 6 9 7 278 250 12.02 11.70 162 Tubulin alpha-8 chain Q6AY56 gi|55976167 5 5 136 118 163 Tubulin beta chain P04691 gi|57429 8 7 9 7 252 285 10.02 10.01 164 Tubulin, beta, 2 Q6P9T8 gi|38014578 6 7 7 3 8 6 33 305 279 1.67 4.00 2.00 165 Tumor rejection antigen gp96 Q66HD0 gi|6015101 7 6 11 9 6 5 14 14 94 76 461 435 5.43 3.40 18.13 16.69 166Type II keratin Kb1 Q6IMF3gi|4648501253972 9876712712521.40 10.019.71 167 Type II keratin Kb18 Q6IG05 gi|13272554 3 75 168 Type II keratin Kb2 Q6IG02 gi|46485118 3 3 3 3 121 115 4.00 4.00 169 Type II keratin Kb36 Q6IG03 gi|46485116 5 4 70 70 170Ubiquitin P62989gi|474778201 46125 96 2231772.002.006.01 171 Ubiquitin-conjugating enzyme E2 N Q9EQX9 gi|77417616 1 1 1 1 49 49 2.00 2.00 172 UDP-glucose pyrophosphorylase 2 Q4V8I9 gi|66910575 3 8 7 7 3 39 139 141 6.00 6.00

Mitochondrial 60 kDa heat shock protein, 1 P63039 gi|51702230 7 6 5 4 89 87 4.30 4.09 mitochondrial [Precursor] 2 ADP/ATP translocase 2 Q09073 gi|728810 2 2.00 Aldehyde dehydrogenase, 3 P11884 gi|38541105 2 2 42 42 mitochondrial [Precursor] ATP synthase alpha chain, 4 P15999gi|1145237284 21074444180180 1.336.076.02 mitochondrial [Precursor] [Fragment] ATP synthase beta chain, 5 P10719 gi|114562 8 8 9 7 212 217 11.41 10.86 mitochondrial [Precursor] ATP synthase lipid-binding protein, 6 Q06646 gi|63578751 2 65 mitochondrial [Precursor] ATP synthase, H+ transporting, 7 mitochondrial F1 complex, alpha Q6P753 gi|38512279 2 87 subunit, isoform 1 ATPase, H+ transporting, V1 subunit E 8 Q6PCU2 gi|81892462 2 2 4 45 45 1.40 isoform 1 Carbamoyl-phosphate synthase 9 P07756 gi|203576 9 7 7 4 222 194 8.00 7.30 [ammonia], mitochondrial [Precursor] Carnitine O-palmitoyltransferase I, 10 P32198 gi|416835 3 1 6 1 53 53 2.00 2.00 mitochondrial liver isoform Cytochrome c1, heme protein, Q9D0M3 11 gi|21759079 2 2 2 1 43 43 2.00 2.00 mitochondrial [Precursor] mouse D-beta-hydroxybutyrate 12 dehydrogenase, mitochondrial P29147 gi|203921 3 2 4 1 60 60 2.00 2.00 [Precursor] Electron transfer flavoprotein- 13 ubiquinone oxidoreductase, Q6UPE1 gi|52000614 1 32 mitochondrial [Precursor] 14Microsomal glutathione S-transferase 1P08011gi|38649092325422641691524453922.012.018.008.00 Mitochondrial aldehyde dehydrogenase 15 Q6Q288 gi|45737868 2 42 [Fragment] Phospholipid hydroperoxide 16 glutathione peroxidase, mitochondrial P36970 gi|1041645 2 2 4 49 49 2.00 [Precursor], nuclear 17 Prohibitin-2 Q5XIH7 gi|76363296 2 1 2.00 2.00 Pyruvate carboxylase, mitochondrial 18 P52873 gi|1709948 6 12 5 40 2.03 2.01 [Precursor] similar to tetratricopeptide repeat 19 - gi|27664028 1 1 42 42 domain 11 Thiosulfate sulfurtransferase 20 P24329 gi|135826 4 2 1 34 2.00 1.70 [Fragment] Trans-2-enoyl-CoA reductase, 21 Q9Z311 gi|62900383 2 33 mitochondrial [Precursor] Trifunctional enzyme alpha subunit, 22 Q64428 gi|2494234 2 2 55 55 mitochondrial [Precursor] Vacuolar ATP synthase catalytic P50516 23 gi|1718086 4 5 8 155 149 8.01 subunit A, ubiquitous isoform mouse Voltage-dependent anion-selective 24 P81155 gi|46397780 3 2 2 2 51 51 2.00 1.31 channel protein 2

Nuclear 1 Basic transcription factor 3 Q5U3Y8 gi|81883573 2 2 43 43 CCAAT displacement protein 2 P53565 gi|1705737 13 16 18 17 278 321 11.68 15.13 [Fragment] Damage-specific DNA binding protein 3 Q9ESW0 gi|9843869 11 9 6 4 75 70 5.41 4.18 1 4 DEAD-box protein 3, Y-chromosomal Q62095 gi|55562828 2 48 5 DNA mismatch repair protein Msh2 P54275 gi|1709122 4 39 Double-stranded RNA-binding protein 6 Q68SB1 gi|19526444 3 1.40 Staufen homolog 2 Heterogeneous nuclear 7 P61980 gi|48429097 3 3 3 1 85 85 2.01 2.00 ribonucleoprotein K 8 Histone H2A, testis Q00728 gi|399852 3 1 39 2.00 9 Histone H4 P62804 gi|51317315 1 1 36 2.47 10 Hypothetical LOC305240 Q6AY21 gi|50927029 4 1 1.41 1.30 Lamina-associated polypeptide 2 11 Q62733 gi|46576200 4 3 6 3 45 45 2.00 2.00 isoform beta 12 NSFL1 cofactor p47 O35987 gi|41017427 2 2 2 53 53 1.40 Nuclear transcription factor Y subunit 13 P63140 gi|203353 1 1.30 beta Nuclease sensitive element binding 14 P62961 gi|51704186 1 2 3 1 59 59 2.01 2.00 protein 1 Q8BJW5 15 Nucleolar protein 11 gi|73921239 3 35 mouse P55201 16 Peregrin gi|1705500 4 36 human Peroxisome proliferator-activated 17 P37230 gi|585718 3 1.40 receptor alpha Phospholipid hydroperoxide 18 glutathione peroxidase, mitochondrial P36970 gi|1041645 2 2 4 49 49 2.00 [Precursor], nuclear 19 Poly(RC) binding protein 2 Q6AYU5 gi|50926841 3 5 4 5 56 191 176 9.40 20 Regulator of G-protein signaling 12 O08774 gi|2500169 9 1.42 21 RuvB-like 2 Q4QQS4 gi|67678298 5 2 2.00 2.00 22 Structural maintenance of chromosome Q8CG48 gi|30173243 9 34 2-like 1 protein mouse 23 Tceb3 protein Q66HK4 gi|51859136 2 82 Q62383 24 Transcription elongation factor SPT6 gi|51701937 7 42 mouse 25 Transcription factor HES-1 Q04666 gi|547626 2 1 2.00 1.70 26 Ubiquitin-fold modifier 1 [Precursor] Q5BJP3 gi|60688529 1 1 50 50

Peroxisomal Acyl-coenzyme A oxidase 2, 1 P97562 gi|17365975 4 3 4 3 58 58 2.05 2.01 peroxisomal Bile acid CoA:amino acid N- 2 Q63276 gi|604902 1 1 2 53 75 2.48 acyltransferase 3 Catalase P04762 gi|115707 6 5 4 4 116 110 4.97 2.00 4 Peroxisomal bifunctional enzyme P07896 gi|119120 2 2 92 2.00 Peroxisomal multifunctional enzyme 5 P97852 gi|1881831 2 10 9 8 7 38 161 171 12.01 11.00 type 2 Phytanoyl-CoA dioxygenase, 6 P57093 gi|55824682 2 2 3 2 63 67 3.40 3.30 peroxisomal [Precursor] 7Uricase P09118gi|1371082132 2250507675 4.004.00 8Very-long-chain acyl-CoA synthetaseP97524gi|318319932754 6542421551531.41 7.667.22

Contaminant 1Hemoglobin alpha-1/2 subunit P01946gi|3774807522432 23544648482.04 2.592.24 2Hemoglobin beta-1 subunit P02091gi|3484961811323 23696972662.00 2.002.00 3 Hemoglobin beta-2 subunit P11517 gi|122529 3 2 3 51 51 4.00 P35527 4 Keratin, type I cytoskeletal 9 gi|81175178 2 34 human P00761 5 Trypsin [Precursor] gi|136429333442545294215494134.004.005.704.52 pig Supplementary Table 2. List of identified proteins with two or more transmembrane sequences. TM-analysis were done using the TMHMM prediction program

TM Protein Name of the protein Accession number domains class NCBI TMHMM SwissProt 2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor gi|1168907 Q09426 2 ? 3-oxo-5-alpha-steroid 4-dehydrogenase 1 gi|206838 P24008 3 Microsomal 7-dehydrocholesterol reductase gi|51859408 Q9Z2Z8 6 ER Ab1-205 gi|33086478 Q7TP91 7 ER Membrane ABC transporter ABCG3 gi|51243003 Q68HW7 5 assosiated Acetyl-CoA transporter gi|7768591 Q9JM68 9 ? ADP/ATP translocase 2 gi|728810 Q09073 2 Mitochondrial Membrane Amyloid-like protein 2 [Precursor] gi|1703345 P15943 2 assosiated Membrane Anion exchange protein 2 gi|114792 P23347 11 assosiated Plasma Anion exchange protein 3 gi|114782 P23348 11 membrane Arylacetamide deacetylase gi|57012548 Q9QZH8 2 ER ATP synthase lipid-binding protein, mitochondrial [Precursor] gi|63578751 Q06646 2 Mitochondrial Membrane ATPase 7B [Fragment] gi|6006291 Q9R0T2 5 assosiated ATPase, H+ transporting, lysosomal (vacuolar proton pump) noncat gi|77627990 - 6 ? Membrane ATP-binding cassette sub-family G member 8 gi|38258880 P58428 6 assosiated Plasma Band 3 anion transport protein gi|20141169 P23562 10 membrane Membrane Bile salt export pump gi|12585136 O70127 9 assosiated Calcium-transporting ATPase type 2C member 1 gi|202864 Q64566 8 Golgi Membrane Canalicular multispecific organic anion transporter 1 gi|1405353 Q63120 14 assosiated Membrane Cationic amino acid transporter-2 gi|67942063 Q4PLF2 14 assosiated Membrane Cc1-3 gi|62990119 Q7TP16 6 assosiated Cop-coated vesicle membrane protein p24 [Precursor] gi|3914232 Q63524 2 Transport Copper-transporting ATPase 2 gi|312172 Q64535 7 Golgi Cytochrome P450 2D1 gi|117241 P10633 2 ER Cytochrome P450 2D3 gi|3915646 P12938 2 ER Cytochrome P450 2D5 gi|117245 P12939 2 ER Cytochrome P450 3A1 gi|117153 P04800 2 ER Cytochrome P450 3A2 gi|6166033 P05183 3 ER Cytochrome P450 4A1 gi|117163 P08516 2 ER Cytochrome P450 4A3 [Precursor] gi|1352184 P20817 2 ER Membrane Cytochrome P450, 4a10 gi|27819673 Q642E9 2 assosiated Cytochrome P450, family 2, subfamily d, polypeptide 9 gi|50925431 Q6AZ78 2 Microsomal DAMP-1 protein gi|28070980 Q811A2 2 ? Deleted in polyposis 1-like 1 gi|54035487 Q5XI60 3 Unknown Membrane Delta-5 fatty acid desaturase gi|15823618 Q920R3 3 assosiated Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa gi|38051929 P25235 3 ER subunit [Precursor] Dolichyl-di-phosphooligosaccharide-protein glycotransferase gi|51980337 Q641Y0 2 ER Ectonucleoside triphosphate diphosphohydrolase 5 gi|38303951 Q6P6S9 2 ? Plasma Epidermal growth factor receptor gi|6478868 Q9QX70 2 membrane? Q9DC16 ER-Golgi intermediate compartment 32 kDa protein gi|52000733 2ERGIC mouse Membrane Estradiol 17-beta-dehydrogenase 2 gi|3334165 Q62730 2 assosiated Furin [Precursor] gi|56172 P23377 2 Golgi Plasma G protein-coupled receptor 50 gi|34881847 - 7 membrane? Glucose-6-phosphatase gi|567864 P43428 9 ER Membrane HIG1 domain family member 1A gi|76363184 Q8VH49 2 assosiated Q80TN5 Huntingtin-interacting protein 14 gi|46395762 6 Golgi mouse Hypothetical LOC312135 gi|56268908 Q5PQM0 9 Unknown Hypothetical protein gi|71680968 Q497A2 10 Golgi? Hypothetical protein MGC116126 gi|67678472 Q4QQU5 5 Unknown hypothetical protein XP_217094 gi|27719651 - 4 Unknown hypothetical protein XP_219337 gi|62641295 - 2 Unknown Membrane Interferon-inducible protein gi|124492 P26376 2 assosiated LIM homeobox protein 3 (predicted) gi|62644770 - 2 ? Lipid phosphate phosphohydrolase 3 gi|1684745 P97544 6 ER Membrane Liver-specific transport protein gi|529590 Q63314 11 assosiated LOC170824 protein gi|55715850 Q5RKL5 5 Unknown LRRGT00110 gi|56268893 Q6TUD4 5 Unknown Membrane L-type calcium channel alpha-1c subunit gi|17864840 Q8VHT2 19 assosiated Lysosomal acid phosphatase [Precursor] gi|130729 P20611 2 Lysosomal Lysosome membrane protein II gi|38197654 P27615 2 Lysosomal Membrane MAL2A gi|32693285 Q7TPB7 4 assosiated mannosidase 1, alpha gi|75905483 - 2 Golgi Microsomal/ Microsomal glutathione S-transferase 1 gi|38649092 P08011 3 Mitochondrial gi|17736804 Q8VIF1 Mid-1-related chloride channel 2; Mid-1-related chloride channel 1; gi|14278955 Q9WU61 4ER/Golgi LOC170927 protein gi|51858922 Q66HQ5 Membrane Multidrug resistance protein 1a gi|7739773 Q9JK64 11 assosiated Membrane Multidrug resistance-associated protein 5 gi|11133307 Q9QYM0 11 assosiated Membrane Myeloid-associated differentiation marker gi|33590376 Q6VBQ5 8 assosiated Membrane Na-K-Cl cotransporter gi|13929130 Q9QX10 12 assosiated Plasma Neu protooncoprotein gi|81866669 Q8K3F9 2 membrane? Nicalin [Precursor] gi|67460594 Q5XIA1 2 ER Membrane olfactory receptor Olr170 gi|47576697 - 7 assosiated Orphan sodium- and chloride-dependent neurotransmitter transporter Membrane gi|730198 Q08469 12 NTT73 assosiated Membrane P-glycoprotein sister gi|3273484 O88331 9 assosiated Phosphoinositide phosphatase SAC1 gi|11095248 Q9ES21 2 ? Membrane Potassium-transporting ATPase alpha chain 1 gi|203037 P09626 8 assosiated Membrane Potassium-transporting ATPase alpha chain 2 gi|1703464 P54708 8 assosiated ER/ PRA1 family protein 3 gi|38494360 Q9ES40 4 Transport? Prenylated Rab acceptor protein 1 gi|55562836 O35394 2 Golgi Q8TF62 Membrane Probable phospholipid-transporting ATPase IM gi|30315933 9 human assosiated RGD1306324_predicted protein gi|71681283 Q498C8 3 Golgi? gi|63641883 RIKEN cDNA 3110004L20 - 11 Unknown mouse Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 gi|9789714 Q64578 7 ER Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 gi|114315 P11507 8 ER Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 gi|114316 P18596 8 ER Sec22 homolog gi|51980493 Q642F4 4 Transport secretory carrier membrane protein 3 (predicted) gi|34857962 - 4 Transport? Secretory carrier-associated membrane protein 1 gi|3914958 P56603 4 Transport? Secretory carrier-associated membrane protein 4 gi|47116975 Q9ET20 4 Transport? similar to 1110065L07Rik protein gi|62662993 - 2 Unknown similar to 1810073N04Rik protein gi|62657470 - 9 Unknown similar to ARL6IP2 gi|62650248 - 2 Transport? similar to ATPase, Class VI, type 11C isoform a gi|62667482 - 7 ? similar to ATP-binding cassette transporter sub-family A member 6 gi|62657287 - 12 ? similar to ATP-binding cassette transporter sub-family A member 8a gi|62657283 - 14 ? similar to ATP-binding cassette, subfamily G, member 3 gi|62660110 - 5 ? similar to brain-specific angiogenesis inhibitor 2 gi|62649735 - 8 ? similar to centaurin, gamma 2 gi|62655381 - 2 Transport Similar to choline phosphotransferase 1; cholinephosphotransferase 1 gi|56090323 Q66H21 8 ? alpha; cholinephosphotransferase 1 similar to collagen type XVII gi|62642454 - 2 ? similar to ectonucleoside triphosphate diphosphohydrolase 4 gi|62661681 - 2 Golgi similar to Expressed sequence AI788959 gi|62660356 - 2 Unknown Membrane similar to expressed sequence AI790205 gi|62644915 - 7 assosiated? similar to FLJ16237 protein gi|62650633 - 3 Unknown similar to G protein-coupled receptor 89 gi|62643936 - 7 ? similar to GPI7 gi|62660028 - 11 ? similar to hypothetical protein 6030458H05 gi|62662365 - 10 Unknown similar to hypothetical protein FLJ14681 gi|62645841 - 7 Unknown similar to hypothetical protein MGC5391 gi|62664164 - 4 Unknown similar to major facilitator superfamily domain containing 1 gi|62643542 - 11 ? similar to Microsomal glutathione S-transferase 2 (Microsomal GST-2) gi|27690924 - 2 ? (Microsomal GST-II) Membrane similar to PL6 protein gi|34865897 - 8 assosiated similar to Protein HSPC163 gi|27679416 - 3 ? similar to RIKEN cDNA 1810036I24 gi|34861791 - 3 Unknown similar to RIKEN cDNA 2310008M10 gi|62644383 - 3 Unknown Similar to RIKEN cDNA 2310034L04 gi|81883039 Q5M7T4 5 Unknown similar to RIKEN cDNA 2510039O18 gi|34872456 - 2 Unknown similar to RIKEN cDNA 5730596K20 gi|62641830 - 2 Unknown similar to RIKEN cDNA A930025J12 gi|62645640 - 6 Unknown similar to RIKEN cDNA B230339H12 gi|62662951 - 8 Unknown similar to scavenger receptor type A SR-A gi|62662711 - 2 ? similar to serine/threonine kinase gi|62659973 - 3 ? similar to solute carrier family 30 (zinc transporter), member 6 gi|62650354 - 6 ? similar to solute carrier family 35, member E2 gi|62650165 - 8 ? similar to squamous cell carcinoma antigen recognized by T cells 2 gi|62666043 - 2 ? similar to Transmembrane emp24 protein transport domain containing 4 gi|27697481 - 2 ER Membrane similar to transmembrane protein TM9SF3 gi|34862730 - 9 assosiated similar to UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- gi|62665443 - 3 Golgi? acetylgalactosaminyltransferase 2 Membrane similar to zinc finger, DHHC domain containing 13 gi|62639789 - 7 assosiated similar to zinc transporter 5 gi|62642842 - 15 ? SLC10A5 gi|70608094 Q4JLT5 9 ? Membrane Slc30a7_predicted protein [Fragment] gi|60688531 Q5BJM8 2 assosiated Membrane Sodium/bile acid cotransporter gi|127792 P26435 7 assosiated Membrane Sodium/potassium-transporting ATPase alpha-1 chain [Precursor] gi|38303881 P06685 10 assosiated Plasma Sodium/potassium-transporting ATPase alpha-2 chain [Precursor] gi|114379 P06686 8 membrane Membrane Sodium/potassium-transporting ATPase alpha-4 chain gi|18202605 Q64541 10 assosiated Plasma Solute carrier family 2, facilitated glucose transporter member 2 gi|121758 P12336 11 membrane Plasma Solute carrier family 23 member 1 gi|24212394 Q9WTW7 10 membrane Solute carrier family 27 (Fatty acid transporter), member 32 gi|3087820 Q66HN6 2 ? Solute carrier family 4 sodium bicarbonate cotransporter-like member 10 Membrane gi|46361421 Q6PU72 11 rb5NCBE assosiated Sterol regulatory element binding protein 1 [Fragment] gi|17380503 P56720 2 ER/Golgi Membrane Sulfate anion transporter 1 gi|1173364 P45380 9 assosiated Membrane Synaptic glycoprotein SC2 gi|37589607 Q64232 4 assosiated Synaptophysin-like protein gi|51859315 Q66H18 3 Transport? Plasma System N amino acid transporter 1 gi|51859110 Q9JHZ9 11 membrane T-cell immunomodulatory protein [Precursor] gi|45477218 Q8R4E1 2 Cargo T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 gi|62641689 - 6 ? protein a isoform 3 TORID gi|37590771 Q925D4 4 ? TPA regulated locus gi|66911475 Q4V899 7 Cargo? Membrane Transmembrane 7 superfamily member 2 gi|60551458 Q5BK21 7 assosiated Membrane Transmembrane 9 superfamily protein member 1 [Precursor] gi|62287546 Q66HF2 8 assosiated Transmembrane 9 superfamily protein member 2 [Precursor] gi|62287547 Q66HG5 9 Endosome Transmembrane 9 superfamily protein member 4 gi|68533829 Q4KLL4 9 ? Transmembrane emp24 domain containing protein 10 [Precursor] gi|1360136 Q63584 2 Golgi UDP-glucuronosyltransferase 1-1 precursor, microsomal gi|2501473 Q64550 2 Microsomal UDP-N-acetylglucosamine transporter gi|59798524 Q6AXR5 8 Golgi Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1 gi|206430 P25286 6 Transport? Very-long-chain acyl-CoA synthetase gi|3183199 P97524 2 Peroxisomal Membrane Voltage-dependent R-type calcium channel alpha-1E subunit gi|1705707 Q07652 19 assosiated Membrane Zinc finger DHHC domain containing protein 7 gi|28202092 Q923G5 4 assosiated