11/29/2010 Rubbia-Brandt et al. 1 Table S1: 613 up-regulated genes in SOS compared to control livers (FDR adjusted p-value ≤ 0.05) Fold- Chang adjusted p-value e (SOS p-value Gene Symbol Name (SOS vs. vs. (SOS vs. Control) Contro Control) l) CCL20 chemokine (C-C motif) ligand 20 10.97 0.0001 0.0142 COL15A1 collagen, type XV, alpha 1 5.42 0.0000 0.0057 DLK1 delta-like 1 homolog (Drosophila) 4.30 0.0002 0.0171 CHI3L1 chitinase 3-like 1 (cartilage glycoprotein-39) 4.14 0.0001 0.0130 CRP C-reactive protein 4.01 0.0127 0.0339 GABBR1 gamma-aminobutyric acid (GABA) B receptor, 1 3.77 0.0001 0.0167 SLC38A1 solute carrier family 38, member 1 3.70 0.0001 0.0155 pleckstrin homology-like domain, family A, PHLDA2 3.66 0.0007 0.0284 member 2 RASD1 RAS, dexamethasone-induced 1 3.65 0.0001 0.0168 FABP4 fatty acid binding protein 4, adipocyte 3.64 0.0000 0.0094 SOD2 superoxide dismutase 2, mitochondrial 3.50 0.0003 0.0205 COL1A2 collagen, type I, alpha 2 3.48 0.0001 0.0157 HBB hemoglobin, beta 3.46 0.0002 0.0173 heat shock protein 90kDa alpha (cytosolic), class HSP90AB1 3.43 0.0032 0.0498 B member 1 VWF von Willebrand factor 3.07 0.0000 0.0110 serpin peptidase inhibitor, clade E (nexin, SERPINE1 3.04 0.0018 0.0390 plasminogen activator inhibitor type fatty acid binding protein 5 (psoriasis- FABP5 3.04 0.0020 0.0412 associated) COL1A1 collagen, type I, alpha 1 3.03 0.0002 0.0171 GDF15 growth differentiation factor 15 3.02 0.0030 0.0487 EGF-containing fibulin-like extracellular matrix EFEMP1 2.99 0.0000 0.0057 protein 1 methylenetetrahydrofolate dehydrogenase MTHFD2 2.99 0.0000 0.0071 (NADP+ dependent) 2, methenyltetrahydrof BIRC3 baculoviral IAP repeat-containing 3 2.99 0.0011 0.0323 CASP4 caspase 4, apoptosis-related cysteine peptidase 2.97 0.0003 0.0206 BCAT1 branched chain aminotransferase 1, cytosolic 2.93 0.0000 0.0087 COL4A1 collagen, type IV, alpha 1 2.92 0.0000 0.0057 Fc fragment of IgG, high affinity Ib, receptor FCGR1B 2.89 0.0001 0.0130 (CD64) IFI16 interferon, gamma-inducible protein 16 2.86 0.0008 0.0300 F2RL1 coagulation factor II (thrombin) receptor-like 1 2.84 0.0015 0.0365 GPNMB glycoprotein (transmembrane) nmb 2.84 0.0009 0.0306 RGS4 regulator of G-protein signaling 4 2.82 0.0000 0.0057 SLC7A1 solute carrier family 7 (cationic amino acid 2.81 0.0001 0.0159 11/29/2010 Rubbia-Brandt et al. 2 transporter, y+ system), member 1 CCL2 chemokine (C-C motif) ligand 2 2.80 0.0009 0.0304 RRM2 ribonucleotide reductase M2 2.78 0.0000 0.0057 LON peptidase N-terminal domain and ring LONRF2 2.77 0.0002 0.0197 finger 2 IL32 interleukin 32 2.72 0.0006 0.0276 NAMPT nicotinamide phosphoribosyltransferase 2.72 0.0016 0.0372 G0S2 G0/G1switch 2 2.69 0.0010 0.0319 THBS2 thrombospondin 2 2.68 0.0000 0.0057 TNC tenascin C 2.64 0.0017 0.0379 CXCR4 chemokine (C-X-C motif) receptor 4 2.63 0.0009 0.0304 tankyrase, TRF1-interacting ankyrin-related TNKS2 2.61 0.0006 0.0272 ADP-ribose polymerase 2 CTHRC1 collagen triple helix repeat containing 1 2.60 0.0001 0.0130 THBS1 thrombospondin 1 2.58 0.0017 0.0379 SGMS2 sphingomyelin synthase 2 2.57 0.0020 0.0412 FRMD6 FERM domain containing 6 2.55 0.0009 0.0304 TNFAIP8 tumor necrosis factor, alpha-induced protein 8 2.53 0.0000 0.0079 EXT1 exostoses (multiple) 1 2.53 0.0025 0.0451 HSPA6 heat shock 70kDa protein 6 (HSP70B') 2.52 0.0007 0.0288 LBP lipopolysaccharide binding protein 2.52 0.0010 0.0320 BAG3 BCL2-associated athanogene 3 2.49 0.0007 0.0277 TOP2A topoisomerase (DNA) II alpha 170kDa 2.47 0.0001 0.0130 GK glycerol kinase 2.45 0.0005 0.0240 HBA1 /// HBA2 hemoglobin, alpha 1 /// hemoglobin, alpha 2 2.41 0.0001 0.0143 STC1 stanniocalcin 1 2.41 0.0000 0.0121 CCT2 chaperonin containing TCP1, subunit 2 (beta) 2.39 0.0022 0.0430 ODC1 ornithine decarboxylase 1 2.38 0.0011 0.0330 ER degradation enhancer, mannosidase alpha- EDEM3 2.38 0.0020 0.0410 like 3 GLIS3 GLIS family zinc finger 3 2.38 0.0002 0.0187 ZNF295 zinc finger protein 295 2.37 0.0023 0.0439 aryl hydrocarbon receptor nuclear translocator- ARNTL2 2.37 0.0016 0.0376 like 2 LOXL4 lysyl oxidase-like 4 2.37 0.0022 0.0427 LOC387763 hypothetical protein LOC387763 2.36 0.0002 0.0171 FAT1 FAT tumor suppressor homolog 1 (Drosophila) 2.36 0.0028 0.0471 methylenetetrahydrofolate dehydrogenase MTHFD1L 2.36 0.0001 0.0130 (NADP+ dependent) 1-like FCGR1A /// Fc fragment of IgG, high affinity Ia, receptor 2.35 0.0001 0.0159 FCGR1C (CD64) /// Fc fragment of IgG, hi procollagen-lysine, 2-oxoglutarate 5- PLOD2 2.34 0.0007 0.0277 dioxygenase 2 serpin peptidase inhibitor, clade B (ovalbumin), SERPINB1 2.34 0.0015 0.0365 member 1 11/29/2010 Rubbia-Brandt et al. 3 NCOA7 nuclear receptor coactivator 7 2.32 0.0004 0.0224 FNDC3B fibronectin type III domain containing 3B 2.29 0.0010 0.0314 CHSY3 chondroitin sulfate synthase 3 2.29 0.0012 0.0340 C12orf5 chromosome 12 open reading frame 5 2.28 0.0000 0.0130 CD69 CD69 molecule 2.28 0.0004 0.0230 GTP binding protein overexpressed in skeletal GEM 2.28 0.0011 0.0328 muscle CH25H cholesterol 25-hydroxylase 2.28 0.0011 0.0331 SOCS1 suppressor of cytokine signaling 1 2.27 0.0089 0.0491 PALLD palladin, cytoskeletal associated protein 2.26 0.0028 0.0469 DTL denticleless homolog (Drosophila) 2.26 0.0004 0.0226 TIMP1 TIMP metallopeptidase inhibitor 1 2.26 0.0000 0.0109 LOXL2 lysyl oxidase-like 2 2.25 0.0000 0.0057 serpin peptidase inhibitor, clade B (ovalbumin), SERPINB8 2.25 0.0012 0.0342 member 8 GPATCH4 G patch domain containing 4 2.25 0.0008 0.0300 LUM lumican 2.25 0.0004 0.0224 TOP1 topoisomerase (DNA) I 2.24 0.0019 0.0407 CTSC cathepsin C 2.24 0.0029 0.0478 potassium channel tetramerisation domain KCTD14 2.23 0.0028 0.0473 containing 14 PTGFRN prostaglandin F2 receptor negative regulator 2.23 0.0000 0.0124 VCAN versican 2.22 0.0026 0.0454 FBN1 fibrillin 1 2.22 0.0003 0.0221 MAP1B microtubule-associated protein 1B 2.22 0.0000 0.0083 ARL5B ADP-ribosylation factor-like 5B 2.22 0.0025 0.0449 COL4A2 collagen, type IV, alpha 2 2.21 0.0001 0.0141 STK17A serine/threonine kinase 17a 2.21 0.0006 0.0276 integrin, beta 1 (fibronectin receptor, beta ITGB1 2.20 0.0031 0.0492 polypeptide, antigen CD29 includes CSDA cold shock domain protein A 2.20 0.0003 0.0205 UDP-GlcNAc:betaGal beta-1,3-N- B3GNT5 2.19 0.0001 0.0159 acetylglucosaminyltransferase 5 VIM vimentin 2.18 0.0005 0.0241 pro-platelet basic protein (chemokine (C-X-C PPBP 2.17 0.0004 0.0235 motif) ligand 7) ATR ataxia telangiectasia and Rad3 related 2.17 0.0015 0.0367 IFNGR1 interferon gamma receptor 1 2.16 0.0006 0.0276 MKI67 (FHA domain) interacting nucleolar MKI67IP 2.16 0.0004 0.0236 phosphoprotein DDX21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 2.15 0.0016 0.0372 SLC35C1 solute carrier family 35, member C1 2.15 0.0015 0.0365 GOLM1 golgi membrane protein 1 2.15 0.0004 0.0226 XAF1 XIAP associated factor 1 2.14 0.0008 0.0297 HSPA2 heat shock 70kDa protein 2 2.13 0.0003 0.0205 11/29/2010 Rubbia-Brandt et al. 4 interleukin 6 signal transducer (gp130, IL6ST 2.13 0.0120 0.0313 oncostatin M receptor) ANXA2 annexin A2 2.13 0.0001 0.0161 THBD thrombomodulin 2.13 0.0000 0.0130 apolipoprotein B mRNA editing enzyme, APOBEC3B 2.13 0.0003 0.0204 catalytic polypeptide-like 3B protein phosphatase 2, regulatory subunit B', PPP2R5E 2.13 0.0004 0.0235 epsilon isoform PBK PDZ binding kinase 2.13 0.0001 0.0141 TNFAIP3 tumor necrosis factor, alpha-induced protein 3 2.12 0.0006 0.0272 PLSCR1 phospholipid scramblase 1 2.12 0.0007 0.0287 DTNA dystrobrevin, alpha 2.12 0.0029 0.0478 NRP1 neuropilin 1 2.12 0.0014 0.0360 COL3A1 collagen, type III, alpha 1 2.12 0.0004 0.0223 LOC286434 hypothetical protein LOC286434 2.11 0.0007 0.0286 pregnancy-associated plasma protein A, PAPPA 2.11 0.0000 0.0065 pappalysin 1 DKC1 dyskeratosis congenita 1, dyskerin 2.11 0.0003 0.0221 NARG1 NMDA receptor regulated 1 2.10 0.0028 0.0471 TMEM165 transmembrane protein 165 2.09 0.0001 0.0153 CLEC7A C-type lectin domain family 7, member A 2.09 0.0032 0.0498 LOC100288985 hypothetical protein LOC100288985 2.09 0.0008 0.0292 structural maintenance of chromosomes flexible SMCHD1 2.09 0.0017 0.0384 hinge domain containing 1 karyopherin alpha 2 (RAG cohort 1, importin KPNA2 2.08 0.0001 0.0167 alpha 1) MINA MYC induced nuclear antigen 2.08 0.0016 0.0369 ETV6 ets variant 6 2.08 0.0013 0.0345 IER5 immediate early response 5 2.08 0.0002 0.0194 eukaryotic translation elongation factor 1 EEF1E1 2.07 0.0006 0.0265 epsilon 1 IGSF6 immunoglobulin superfamily, member 6 2.07 0.0021 0.0425 FAM169B family with sequence similarity 169, member B 2.06 0.0019 0.0402 LGALS3 lectin, galactoside-binding, soluble, 3 2.06 0.0007 0.0276 tumor necrosis factor receptor superfamily, TNFRSF10A 2.05 0.0007 0.0276 member 10a v-myc myelocytomatosis viral oncogene MYC 2.05 0.0025 0.0450 homolog (avian) EHBP1L1 EH domain binding protein 1-like 1 2.05 0.0001 0.0137 solute carrier family 6 (neurotransmitter SLC6A6 2.05 0.0000 0.0057 transporter, taurine), member 6 RAB27A RAB27A, member RAS oncogene family 2.05 0.0004 0.0229 GAS2L3 Growth arrest-specific 2 like 3 2.04 0.0001 0.0130 GJC1 gap junction protein, gamma 1, 45kDa 2.04 0.0000 0.0094 11/29/2010 Rubbia-Brandt et al.