Table 3.
Summary of differentially expressed genes of CYPs, non-CYP phase I enzymes, phase II enzymes, and transporters.
| Liver |
Proximal small intestine |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Ensembl ID | Fold change (log2) | Adjusted P-value | Gene | Ensembl ID | Fold change (log2) | Adjusted P-value | Gene | Ensembl ID | Fold change (log2) | Adjusted P-value |
| Down-regulated genes | |||||||||||
| Phase I, CYPs | |||||||||||
| Cyp2c44 | ENSMUSG00000025197 | −0.61 | 5.48E-05 | Cyp8b1 | ENSMUSG00000050445 | −1.23 | 1.77E-06 | Cyp3a11 | ENSMUSG00000056035 | −0.77 | 1.36E-02 |
| Cyp2c67 | ENSMUSG00000062624 | −0.63 | 1.12E-03 | Cyp2u1 | ENSMUSG00000027983 | −1.23 | 5.07E-06 | Cyp2b10 | ENSMUSG00000030483 | −0.82 | 2.74E-03 |
| Cyp2d9 | ENSMUSG00000068086 | −0.68 | 3.96E-04 | Cyp4v3 | ENSMUSG00000079057 | −1.27 | 2.73E-16 | Cyp2c55 | ENSMUSG00000025002 | −1.09 | 2.39E-03 |
| Cyp3a59 | ENSMUSG00000061292 | −0.69 | 1.49E-02 | Cyp2f2 | ENSMUSG00000052974 | −1.30 | 1.48E-14 | Cyp2c65 | ENSMUSG00000067231 | −1.12 | 2.91E-10 |
| Cyp1a2 | ENSMUSG00000032310 | −0.75 | 2.12E-03 | Cyp3a11 | ENSMUSG00000056035 | −1.62 | 5.71E-22 | Cyp2c66 | ENSMUSG00000067229 | −1.61 | 2.84E-10 |
| Cyp2c37 | ENSMUSG00000042248 | −0.92 | 1.49E-05 | Cyp4b1 | ENSMUSG00000028713 | −1.63 | 9.87E-10 | Cyp2c29 | ENSMUSG00000003053 | −2.28 | 2.68E-18 |
| Cyp2c38 | ENSMUSG00000032808 | −0.97 | 2.81E-03 | Cyp2a5 | ENSMUSG00000005547 | −2.70 | 4.57E-51 | ||||
| Cyp2c29 | ENSMUSG00000003053 | −0.98 | 2.13E-06 | Cyp4a12b | ENSMUSG00000078597 | −3.05 | 6.28E-32 | ||||
| Cyp3a25 | ENSMUSG00000029630 | −1.06 | 1.94E-09 | Cyp4a12a | ENSMUSG00000066071 | −3.18 | 5.09E-54 | ||||
| Phase I, Non-CYP | |||||||||||
| Aadac | ENSMUSG00000027761 | −1.10 | 3.95E-18 | Ces1f | ENSMUSG00000031725 | −1.21 | 3.78E-09 | Ces2g | ENSMUSG00000031877 | −0.82 | 1.06E-07 |
| Akr1c19 | ENSMUSG00000071551 | −0.77 | 9.31E-03 | Ces2a | ENSMUSG00000055730 | −1.05 | 1.57E-16 | Ces2b | ENSMUSG00000050097 | −1.36 | 5.96E-06 |
| Aldh1b1 | ENSMUSG00000035561 | −0.60 | 2.17E-03 | Ces2c | ENSMUSG00000061825 | −2.87 | 1.48E-11 | Fmo1 | ENSMUSG00000040181 | −1.59 | 3.50E-10 |
| Aldh3a2 | ENSMUSG00000010025 | −2.17 | 3.97E-45 | Ces2e | ENSMUSG00000031886 | −1.44 | 3.67E-22 | ||||
| Aldh5a1 | ENSMUSG00000035936 | −0.69 | 1.96E-05 | Ces3b | ENSMUSG00000062181 | −1.18 | 1.15E-18 | ||||
| Aldh7a1 | ENSMUSG00000053644 | −0.65 | 5.33E-06 | Dpyd | ENSMUSG00000033308 | −0.59 | 1.26E-03 | ||||
| Aldh9a1 | ENSMUSG00000026687 | −0.59 | 7.45E-05 | Ephx1 | ENSMUSG00000038776 | −1.03 | 1.18E-10 | ||||
| Aox1 | ENSMUSG00000063558 | −0.92 | 1.65E-08 | Ephx2 | ENSMUSG00000022040 | −1.20 | 4.39E-22 | ||||
| Aox3 | ENSMUSG00000064294 | −0.91 | 4.28E-10 | Maob | ENSMUSG00000040147 | −0.80 | 3.04E-06 | ||||
| Cela1 | ENSMUSG00000023031 | −1.19 | 2.30E-06 | Nqo2 | ENSMUSG00000046949 | −0.91 | 6.15E-08 | ||||
| Ces1e | ENSMUSG00000061959 | −1.68 | 1.15E-27 | Suox | ENSMUSG00000049858 | −0.86 | 1.34E-10 | ||||
| Phase II | |||||||||||
| Gstk1 | ENSMUSG00000029864 | −0.59 | 5.30E-05 | Ugt2b36 | ENSMUSG00000070704 | −0.87 | 6.51E-08 | Gstm4 | ENSMUSG00000027890 | −0.95 | 6.82E-05 |
| Gstp1 | ENSMUSG00000060803 | −0.92 | 2.42E-04 | Ugt1a5 | ENSMUSG00000089943 | −0.93 | 1.58E-04 | Gstm3 | ENSMUSG00000004038 | −1.19 | 4.98E-05 |
| Gstm4 | ENSMUSG00000027890 | −0.93 | 1.88E-07 | Ugt2a3 | ENSMUSG00000035780 | −0.96 | 3.08E-09 | ||||
| Gstm2 | ENSMUSG00000040562 | −1.14 | 2.21E-06 | Ugt2b35 | ENSMUSG00000035811 | −1.06 | 1.12E-10 | ||||
| Gstm1 | ENSMUSG00000058135 | −1.14 | 2.24E-17 | Ugt2b5 | ENSMUSG00000054630 | −1.33 | 1.25E-20 | ||||
| Gstt1 | ENSMUSG00000001663 | −1.21 | 8.14E-13 | Ugt1a9 | ENSMUSG00000090175 | −1.61 | 1.29E-17 | ||||
| Gstm6 | ENSMUSG00000068762 | −1.32 | 2.20E-19 | Ugt2b1 | ENSMUSG00000035836 | −2.00 | 1.60E-32 | ||||
| Gstm3 | ENSMUSG00000004038 | −1.74 | 6.21E-16 | Ugt2b38 | ENSMUSG00000061906 | −2.83 | 3.65E-21 | ||||
| Gstt3 | ENSMUSG00000001665 | −1.88 | 9.72E-12 | Sult1b1 | ENSMUSG00000029269 | −0.70 | 6.82E-03 | ||||
| Gstt2 | ENSMUSG00000033318 | −1.89 | 1.66E-17 | Gclc | ENSMUSG00000032350 | −0.82 | 1.29E-08 | ||||
| Gsta4 | ENSMUSG00000032348 | −2.16 | 1.91E-36 | Papss2 | ENSMUSG00000024899 | −1.04 | 1.53E-05 | ||||
| Gsta2 | ENSMUSG00000057933 | −3.45 | 4.19E-45 | Ugp2 | ENSMUSG00000001891 | −1.42 | 5.63E-20 | ||||
| Ugt3a1 | ENSMUSG00000072664 | −0.71 | 3.56E-06 | ||||||||
| ABC Transporters | |||||||||||
| Abca2 | ENSMUSG00000026944 | −0.75 | 3.40E-06 | Abcc9 | ENSMUSG00000030249 | −1.02 | 7.68E-07 | ||||
| Abcb11 | ENSMUSG00000027048 | −0.85 | 8.91E-11 | Abcg5 | ENSMUSG00000040505 | −1.04 | 3.88E-10 | ||||
| Abca8a | ENSMUSG00000041828 | −0.97 | 6.72E-06 | Abcc3 | ENSMUSG00000020865 | −1.19 | 6.18E-09 | ||||
| Abcb4 | ENSMUSG00000042476 | −0.98 | 2.28E-10 | Abcd3 | ENSMUSG00000028127 | −1.25 | 1.15E-14 | ||||
| Abcg8 | ENSMUSG00000024254 | −1.02 | 5.16E-09 | ||||||||
| SLC and SLCO transporters | |||||||||||
| Slc1a2 | ENSMUSG00000005089 | −0.59 | 2.89E-04 | Slc25a22 | ENSMUSG00000019082 | −0.85 | 3.27E-07 | Slc9a2 | ENSMUSG00000026062 | −0.64 | 3.44E-02 |
| Slc6a6 | ENSMUSG00000030096 | −0.59 | 3.45E-03 | Slc35g1 | ENSMUSG00000044026 | −0.90 | 5.12E-05 | Slc5a4a | ENSMUSG00000020229 | −1.12 | 6.46E-09 |
| Slc22a30 | ENSMUSG00000052562 | −0.64 | 1.33E-04 | Slc7a2 | ENSMUSG00000031596 | −0.96 | 2.98E-05 | Slc12a2 | ENSMUSG00000024597 | −1.16 | 4.27E-05 |
| Slc25a10 | ENSMUSG00000025792 | −0.65 | 5.07E-05 | Slc22a28 | ENSMUSG00000063590 | −0.98 | 2.20E-04 | ||||
| Slc25a15 | ENSMUSG00000031482 | −0.67 | 2.80E-06 | Slc17a8 | ENSMUSG00000019935 | −1.10 | 5.62E-04 | ||||
| Slc23a2 | ENSMUSG00000027340 | −0.69 | 2.01E-02 | Slc25a30 | ENSMUSG00000022003 | −1.28 | 1.83E-02 | ||||
| Slc9a3r2 | ENSMUSG00000002504 | −0.74 | 5.31E-03 | Slc43a3 | ENSMUSG00000027074 | −1.33 | 1.50E-10 | ||||
| Slc30a10 | ENSMUSG00000026614 | −0.75 | 7.29E-03 | Slc2a2 | ENSMUSG00000027690 | −1.42 | 4.73E-17 | ||||
| Slc10a1 | ENSMUSG00000021135 | −0.77 | 1.85E-06 | Slc17a4 | ENSMUSG00000021336 | −1.68 | 1.29E-17 | ||||
| Up-regulated genes | |||||||||||
| Phase I, CYPs | |||||||||||
| Cyp2d40 | ENSMUSG00000068083 | 0.66 | 3.48E-04 | Cyp51 | ENSMUSG00000001467 | 0.81 | 1.12E-07 | Cyp2j6 | ENSMUSG00000052914 | 0.83 | 5.46E-03 |
| Cyp39a1 | ENSMUSG00000023963 | 0.68 | 1.77E-02 | Cyp4a31 | ENSMUSG00000028712 | 1.39 | 7.22E-05 | Cyp2j9 | ENSMUSG00000015224 | 0.96 | 4.17E-03 |
| Cyp2c70 | ENSMUSG00000060613 | 0.69 | 2.21E-05 | Cyp3a13 | ENSMUSG00000029727 | 1.54 | 3.07E-28 | ||||
| Cyp17a1 | ENSMUSG00000003555 | 0.75 | 3.29E-02 | ||||||||
| Phase I, Non-CYP | |||||||||||
| Por | ENSMUSG00000005514 | 0.71 | 2.95E-03 | Aldh3b1 | ENSMUSG00000024885 | 0.60 | 7.08E-05 | ||||
| Adh1 | ENSMUSG00000074207 | 0.65 | 9.44E-03 | ||||||||
| Akr1b7 | ENSMUSG00000052131 | 0.67 | 3.96E-02 | ||||||||
| Phase II | |||||||||||
| As3mt | ENSMUSG00000003559 | 0.80 | 1.41E-06 | Papss2 | ENSMUSG00000024899 | 0.70 | 3.77E-02 | ||||
| Papss1 | ENSMUSG00000028032 | 0.66 | 1.38E-02 | Mgst1 | ENSMUSG00000008540 | 0.87 | 5.36E-03 | ||||
| ABC Transporters | |||||||||||
| Abcc6 | ENSMUSG00000030834 | 0.84 | 1.26E-03 | ||||||||
| SLC and SLCO transporters | |||||||||||
| Slc30a1 | ENSMUSG00000037434 | 0.60 | 7.53E-04 | Slc1a4 | ENSMUSG00000020142 | 1.15 | 1.81E-06 | Slc25a28 | ENSMUSG00000040414 | 0.64 | 6.26E-05 |
| Slc46a3 | ENSMUSG00000029650 | 0.62 | 5.90E-03 | Slc13a3 | ENSMUSG00000018459 | 1.26 | 2.07E-09 | Slc19a2 | ENSMUSG00000040918 | 0.81 | 4.79E-06 |
| Slc43a1 | ENSMUSG00000027075 | 0.62 | 2.39E-02 | Slc11a2 | ENSMUSG00000023030 | 1.29 | 3.85E-11 | Slc35e3 | ENSMUSG00000060181 | 0.90 | 1.27E-03 |
| Slc35e3 | ENSMUSG00000060181 | 0.65 | 3.34E-03 | Slc10a2 | ENSMUSG00000023073 | 1.30 | 7.16E-03 | Slc6a3 | ENSMUSG00000021609 | 1.03 | 6.05E-03 |
| Slc41a1 | ENSMUSG00000013275 | 0.65 | 1.97E-02 | Slc17a9 | ENSMUSG00000023393 | 1.31 | 4.59E-05 | ||||
| Slc35b1 | ENSMUSG00000020873 | 0.66 | 7.66E-04 | Slc39a14 | ENSMUSG00000022094 | 1.45 | 5.91E-13 | ||||
| Slc11a1 | ENSMUSG00000026177 | 0.68 | 3.24E-02 | Slc41a2 | ENSMUSG00000034591 | 2.16 | 2.22E-08 | ||||
| Slc25a19 | ENSMUSG00000020744 | 0.76 | 7.18E-04 | Slc13a5 | ENSMUSG00000020805 | 2.19 | 2.24E-14 | ||||
| Slc39a1 | ENSMUSG00000052310 | 0.87 | 4.11E-08 | Slc3a1 | ENSMUSG00000024131 | 2.50 | 6.29E-42 | ||||
| Slc16a12 | ENSMUSG00000009378 | 0.90 | 2.39E-05 | Slc37a1 | ENSMUSG00000024036 | 3.01 | 8.82E-30 | ||||
| Slc30a5 | ENSMUSG00000021629 | 1.00 | 4.26E-09 | ||||||||
Differential gene expression was analyzed by RNA-seq for hepatic and SI RNA samples from mice with or without colitis, as described in Fig. 6. Genes with normalized readout mean > 100, adjusted P-value <0.05, |log2 fold change| >0.585 are presented in various subgroups of drug-metabolizing enzymes and transporters.