Supplementary Data 1. Gene marker sets in each liver toxicity phenotype

TAA&MP: 45 probe sets Probe Set ID Gene Symbol Gene Title UniGene ID 1367648_at Igfbp2 insulin-like growth factor binding protein 2 Rn.6813 1367957_at Rgs3 regulator of G-protein signaling 3 Rn.53900 1368520_at Apoa4 apolipoprotein A-IV Rn.15739 1368530_at Mmp12 matrix metallopeptidase 12 Rn.33193 1368778_at Slc6a6 solute carrier family 6 (neurotransmitter transporter, taurine), member 6 Rn.9968 1369783_a_at Nrg1 neuregulin 1 Rn.37438 1369948_at Ngfrap1 nerve growth factor receptor (TNFRSF16) associated protein 1 Rn.3126 1371237_a_at Mt1a metallothionein 1a Rn.54397 1371735_at ------1372557_at Arl6 ADP-ribosylation factor-like 6 Rn.101944 1372773_at Npdc1 neural proliferation, differentiation and control, 1 Rn.5802 1373499_at Gas5 growth arrest specific 5 Rn.14733 1373658_at Racgap1 Rac GTPase-activating protein 1 Rn.101301 1373814_at R3hdm2 R3H domain containing 2 Rn.203556 1374071_at Fam118a family with sequence similarity 118, member A Rn.36745 1374265_at ------Rn.166593 1374493_at ------Rn.19441 1376100_at Tubb6 tubulin, beta 6 Rn.98430 1377686_at ------Rn.164584 1378413_at ------Rn.146196 1379419_at Tmem184c transmembrane protein 184C Rn.12069 1380533_at App amyloid beta (A4) precursor protein Rn.2104 1382186_a_at Gpatch4 G patch domain containing 4 Rn.20166 1382604_at Polr3g polymerase (RNA) III (DNA directed) polypeptide G Rn.147190 1383434_at Pycr1 pyrroline-5-carboxylate reductase 1 Rn.99704 1383906_at Neurl3 neuralized homolog 3 (Drosophila) Rn.17894 1384449_at ------Rn.11851 1386879_at Lgals3 lectin, galactoside-binding, soluble, 3 Rn.764 1387925_at Asns asparagine synthetase Rn.11172 1388210_at Acot2 acyl-CoA thioesterase 2 Rn.37524 1388666_at Enc1 ectodermal-neural cortex 1 Rn.3039 1388900_at ------1389221_at Mmd2 monocyte to macrophage differentiation-associated 2 Rn.154557 1389230_at ------Rn.4302 1389409_at Tes testis derived transcript Rn.44847 1390232_at RGD1311946 similar to RIKEN cDNA 1810055G02 Rn.16921 1391187_at Ppl periplakin Rn.25259 1392899_at Prc1 protein regulator of cytokinesis 1 Rn.138438 1393252_at ------Rn.165372 1393826_at Apon apolipoprotein N Rn.18716 1394948_at ------Rn.4302 1395557_at ------Rn.166059 1397300_at ------Rn.42112 1397409_s_at Wee1 wee 1 homolog (S. pombe) Rn.208255 1398602_at Mad2l1 MAD2 mitotic arrest deficient-like 1 (yeast) Rn.19771

Supplementary Data 1. (continued) Gene marker sets in each liver toxicity phenotaype

WY&CFB: 52 probe sets Probe Set ID Gene Symbol Gene Title UniGene ID 1367660_at Fabp3 fatty acid binding protein 3, muscle and heart Rn.32566 1367668_a_at Scd stearoyl-CoA desaturase (delta-9-desaturase) Rn.83595 1367742_at Cpt1b carnitine palmitoyltransferase 1b, muscle Rn.6028 1368037_at Cbr1 carbonyl reductase 1 Rn.3425 1368102_at Hsd11b2 hydroxysteroid 11-beta dehydrogenase 2 Rn.10186 1368143_at Anxa7 annexin A7 Rn.106184 1368171_at Lox lysyl oxidase Rn.11372 1368172_a_at Lox lysyl oxidase Rn.11372 1368177_at Acsl3 acyl-CoA synthetase long-chain family member 3 Rn.54820 1368306_at Grin2c glutamate receptor, ionotropic, N-methyl D-aspartate 2C Rn.9709 1368317_at Aqp7 aquaporin 7 Rn.11111 1368453_at Fads2 fatty acid desaturase 2 Rn.162483 1368509_at Bbs2 Bardet-Biedl syndrome 2 Rn.15987 1368544_a_at Nol3 nucleolar protein 3 (apoptosis repressor with CARD domain) Rn.86956 1368888_a_at Rtn4 reticulon 4 Rn.1348 1369973_at Xdh xanthine dehydrogenase Rn.202951 1370043_at Alcam activated leukocyte cell adhesion molecule Rn.5789 1370164_at Hadha hydroxyacyl-Coenzyme A dehydrogenase Rn.3340 1370397_at Cyp4a3 cytochrome P450, family 4, subfamily a, polypeptide 3 Rn.33492 1370605_s_at Lepr leptin receptor Rn.9891 1370803_at Zwint ZW10 interactor Rn.163272 1370813_at Gstm5 glutathione S-transferase, mu 5 Rn.9158 1370818_at Decr2 2,4-dienoyl CoA reductase 2, peroxisomal Rn.144598 1371076_at Cyp2b1 cytochrome P450, family 2, subfamily b, polypeptide 1 Rn.91353 1371223_a_at Lepr leptin receptor Rn.9891 1373564_at Hibch 3-hydroxyisobutyryl-Coenzyme A hydrolase Rn.8745 1373778_at ------Rn.44359 1375900_at Tnfrsf9 tumor necrosis factor receptor superfamily, member 9 Rn.22307 1376191_at Hpgd hydroxyprostaglandin dehydrogenase 15 (NAD) Rn.6386 1377662_at Pir pirin (iron-binding nuclear protein) Rn.103685 1379275_at Snx10 sorting nexin 10 Rn.44192 1382028_at Pex19 peroxisomal biogenesis factor 19 Rn.203104 1383165_at RGD1310209 similar to KIAA1324 protein Rn.22751 1383585_s_at ------1383933_at RGD1308772 similar to KIAA0564 protein Rn.12947 1384580_at C6 complement component 6 Rn.16145 1385574_at RGD1308114 similar to cDNA sequence AF397014 Rn.35332 1386953_at Hsd11b1 hydroxysteroid 11-beta dehydrogenase 1 Rn.888 1386965_at Lpl lipoprotein lipase Rn.3834 1387100_at Aqp3 aquaporin 3 Rn.11109 1387243_at Cyp1a2 cytochrome P450, family 1, subfamily a, polypeptide 2 Rn.5563 1387455_a_at Vldlr very low density lipoprotein receptor Rn.9975 1388199_at Epcam epithelial cell adhesion molecule Rn.106481 1388489_at Ndufa3 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3 Rn.3263 1389611_at Vldlr very low density lipoprotein receptor Rn.9975 1390358_at Cacna2d3 calcium channel, voltage-dependent, alpha2/delta subunit 3 Rn.206369 1390419_a_at Tusc3 tumor suppressor candidate 3 Rn.35146 1390557_at Gca grancalcin Rn.222162 1393933_at Sorl1 sortilin-related receptor, LDLR class A repeats-containing Rn.46267 1394786_at Sorl1 sortilin-related receptor, LDLR class A repeats-containing Rn.46267 1397924_at ------Rn.169405 solute carrier family 25 (carnitine/acylcarnitine translocase), member 1398249_at Slc25a20 Rn.3289 20

Supplementary Data 1.(continued) Gene marker sets in each liver toxicity phenotype

HCB&PB: 10 probe sets Probe Set ID Gene Symbol Gene Title UniGene ID 1368408_at Grk5 G protein-coupled receptor kinase 5 Rn.6500 1368651_at Pklr pyruvate kinase, liver and RBC Rn.48821 1370828_at Zdhhc2 zinc finger, DHHC-type containing 2 Rn.17310 1372297_at Gsta4 glutathione S-transferase alpha 4 Rn.57528 1377161_at ------Rn.34711 1384910_at Lrtm2 leucine-rich repeats and transmembrane domains 2 Rn.34565 1386901_at Cd36 CD36 molecule (thrombospondin receptor) Rn.102418 1387006_at Sult2al1 sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring-like 1 Rn.221887 1388199_at Epcam epithelial cell adhesion molecule Rn.106481 1396035_at Rpesp RPE-spondin Rn.144410