Fig. 2

A and B Analysis of three intermediate GTHC/NGTHCs in rat liver toxicogenomics public data (OPEN TG-GATEs) by PCA with the four genes. Three additional intermediate GTHC/NGTHCs, methapyrilene (MP), monocrotaline (MCT), and thioacetamide (TAA), were analyzed with typical GTHCs, typical NGTHCs and NGTNHCs at 24 h after a single administration [Fig. 2(A)] and at 29 days after repeated administration [Fig. 2(B)] by PCA with four genotoxic marker genes (Bax, Btg2, Ccng1, and Cdkn1). The gene expression profile (log2) was calculated: the mean of each control group was calculated as 0 (log2), and ratio (exp/cont) (log2) was calculated (Appendix B.1 for 24 h and Appendix B.3 for 29 days). These numerical values were analyzed by PCA (Appendix B.2 for 24 h and Appendix B.4 for 29 days). At 24 h, Fig. 2(A) shows the results of 26 chemicals with three doses (low, middle and high), total of 78 points: five typical GTHCs (brown-colored, AAF, AFL, DEN, NNM, and 2NF) were discriminated from seven typical NGTHCs (yellow-colored, CLO, ETH, FEN, GEM, HEX, PHE, and WY) and 11 NGTNHCs (blue-colored, AA, ASP, CAF, CPA, CPP, DEX, DIA, IND, PBZ, THE, and TOL). GTHCs exhibit PC1 below –0.789 (DEN-low; PC1: −0.789, PC2: −1.035). NGTHCs and NGTNHCs exhibit PC1 above −0.334 (IND-high; PC1: −0.334, PC2: 1.355) (Appendix B.2). Speaking of the three intermediates GTHC/NGTHCs (MCT: □, MP: △, and TAA: 〇), TAA-high (PC1: −1.742, PC2: −0.251) is in the GTHCs area (below PC1: −0.789). MP-high (PC1: −0.408, PC2: −0.659), MCT-high (PC1: −0.075, PC2: −0.557) and MP-middle (PC1: 0.747, PC2: –0.79) are in the intermediate area (orange dashed circle). TAA-middle (PCA: 0.135, PC2: −0.173), TAA-low (PC1: 1.101, PC2: −0.385), MP-low (PC1: 0.952, PC2: −0.424), MCT-middle (PC1: 0.851, PC2: −0.231), MCT-high (PC1: 1.043, PC2: −0.47) and MCT-middle (PC1: 0.851, PC2: −0.231) are in the NGTHCs and NGTNHCs area. At 29 days, Fig. 2(B) shows the results of 22 chemical, total of 63 points: two typical GTHCs (brown-colored, AAF-low, -middle, and -high; DEN-low and -high) were discriminated from seven typical NGTHCs (yellow-colored, CLO, ETH, FEN, GEM, HEX, PHE, and WY with three doses) and 10 NGTNHCs (blue-colored, AA, ASP, CAF, CPA, CPP, DIA, PBZ, THE, and TOL with three doses and IND-low and -middle). GTHCs exhibit PC1 below −2.906 (DEN-low). NGTHCs and NGTNHCs exhibit PC1 above 0.001 (CPA-high) (Appendix B.4). Three intermediate GTHC/NGTHCs, MCT-middle (PC1: −4.125, PC2: −0.409), MP-high (PC1: −4.486, PC2: 1.642), TAA-middle (PC1: −3.043, PC2: −0.158), and TAA-high (PC1: −3.667, PC2: 0.274), are in the GTHCs area. In contrast, MCT-low (PC1: −2.279, PC2: −1.467), MP-middle (PC1: −1.403, PC2: −0.398) and TAA-low (PC1: −0.651, PC2: 0.248) are in the intermediate area between GTHCs and NGTHC and NGTNHCs. Only MP-low (PC1: 0.454, PC2: 0.163) is in the NGTHCs and NGTNHCs area. Each group is enclosed with an optional dashed ellipse. Five GTHCs [AAF: 2- acetamidofluorene, AFL: aflatoxin B1, 2NF: 2-nitrofluorene, DEN: N-nitrosodiethylamine and NNM: N-nitrosomorpholine], seven NGTHCs [CLO: clofibrate, ETH: ethanol, FEN: fenofibrate, GEM: gemfibrozil, HEX: hexa-chlorobenzene, PHE: phenobarbital, and WY: WY-14643], 11 NGTNHCs (mostly pharmaceutical drugs) [AA: allyl alcohol, ASP: aspirin, CAF: caffeine, CPA: chlorpheniramine, CPP: chlorpropamide, DEX: dexamethasone, DIA: diazepam, IND: indomethacin, PBZ: phenylbutazone, THE: theophylline, and TOL: tolbutamide] and three intermediate GTHC/NGTHCs [MCT: monocrotaline, MP: methapyrilene, and TAA: thioacetamide]