Microarray analysis of liver: selection of a subset of genes most significantly down-regulated in the untreated Cyp1a1/1a2/1b1(−/−)versus untreated Cyp1(+/+) mouse
These data exclude the Cyp1a1, Cyp1a2, and Cyp1b1 genes, which, because they were genetically ablated, are strikingly (>95-fold) “down-regulated”. Interestingly, one of two Cyp1b1 primer sets that exist in the mouse 70-mer MEEBO oligonucleotide library was detectable and showed up-regulation, but this is interpreted as a genomic transcript that had not been ablated in generating the Cyp1b1(−/−)knockout mouse line (Buters et al., 1999). There were six murine virus genomes significantly (FDR ≤0.10) down-regulated, which were also excluded. False discovery rate is the adjusted P value. One out of ten adjusted P values ≤0.10 would be expected to be a false positive. This is a partial list of 22 selected genes; the entire list of 62 down-regulated genes can be found in the Supplementary Data.
Symbol | Gene Biochemical Name (Likely Function) | -Fold Decrease | P | False Discovery Rate |
|---|---|---|---|---|
| Snora65 | Small nucleolar RNA, H/ACA box-65 (part of ribonucleoprotein complex) | 7.58 | <10−16 | <10−12 |
| St3gal4 a | ST3 β-galactoside α2,3-sialyltransferase (amino-acid glycosylation) | 5.32 | <10−16 | <10−12 |
| Cachd1 | Cache domain-containing-1 (Ca2+-ion binding) | 4.75 | 9 × 10−16 | 2 × 10−12 |
| Rgs16 | Regulator of G protein signaling-16 (GTPase activator, signal transduction) | 4.28 | 10−16 | 2 × 10−11 |
| Cbx3 | Chromobox homolog-3 [Drosophila melanogaster HP1-γ] (chromatinbinding) | 3.89 | 10−11 | 5 × 10−7 |
| Mt2 a | Metallothionein-2 (metal-ion binding) | 3.66 | 5 × 10−12 | 7 × 10−9 |
| Mt1 a | Metallothionein-1 (metal-ion binding) | 3.61 | 2 × 10−13 | 3 × 10−10 |
| Igfbp2 | Insulin-like growth factor-binding protein-2 (growth-factor binding) | 3.33 | 2 × 10−10 | 2 × 10−7 |
| Rbbp4 | Retinoblastoma-binding protein-4 (cell cycle, chromatin modification) | 2.73 | 2 × 10−7 | 0.0001 |
| Ccnd1 | Cyclin D1 (cell cycle, protein kinase regulator) | 2.54 | 4 × 10−9 | 4 × 10−6 |
| Etohd3 | Ethanol decreased-3 (activity in blastocyst) | 2.35 | 0.00023 | 0.037 |
| Il28ra | Interleukin-28 receptor-α (inflammatory signaling pathways) | 2.29 | 0.00004 | 0.0084 |
| Marco | Macrophage receptor with collagenous structure (PO4 transport) | 2.20 | 0.00004 | 0.0098 |
| Snora70 | Small nucleolar RNA, H/ACA box-70 (part of ribonucleoprotein complex) | 2.19 | 0.00004 | 0.0098 |
| Qk | Quaking (axon ensheathment, nucleic-acid binding) | 2.15 | 0.00008 | 0.016 |
| Wee1 | wee-1 homolog [Saccharomyces pombe] (cell cycle, kinase activity) | 2.14 | 0.00007 | 0.015 |
| Ifi27 | Interferon, α-inducible protein 27 (response to virus) | 2.10 | 0.00007 | 0.014 |
| Peci | Peroxisomal Δ3,Δ2-enoyl-coA isomerase (peroxisome assembly, biogenesis) | 2.10 | 0.00007 | 0.015 |
| Trpm8 b | Transient receptor potential cation channel, subfamily M, member 8 (Ca2+ channel activity) | 2.08 | 0.00064 | 0.074 |
| Slco1a1 b | Solute-carrier organic anion transporter family 1, member 1 (organic anion transport) | 2.02 | 0.00010 | 0.018 |
| Socs2 a | Suppressor of cytokine-signaling-2 (chemokine signal transduction, fat cell differentiation) | 1.97 | 0.00035 | 0.048 |
|
Mt4
a
| Metallothionein-4 (metal-ion binding) | 1.91 | 0.00067 | 0.076 |