Table 1. Effects of fat feeding on hepatic transcription of genes contributing to changes in KEGG pathways conserved or divergent in BALB/c and C57BL/6J mice.
| Pathway/Gene |
C57BL/6J
|
BALB/c
|
|||
|---|---|---|---|---|---|
| Symbol | Gene description | TR | P | TR | P |
| Proteasome | |||||
| Psma2 (α2) | Proteasome subunit, alpha type 2 | 1.3 | 0.004 | -1.2 | Ns |
| Psma4 (α3) | Proteasome subunit, alpha type 4 | 1.2 | 0.03 | -1.1 | Ns |
| Psma5 (α5) | Proteasome subunit, alpha type 5 | 1.2 | 0.026 | -1.2 | 0.05 |
| Psma7 (α4) | Proteasome subunit, alpha type 7 | 1.2 | 0.045 | -1.2 | Ns |
| Psmb3 (β3) | Proteasome subunit, beta type 3 | 1.2 | 0.035 | -1.1 | Ns |
| Psmb4 (β7) | Proteasome subunit, beta type 4 | 1.1 | Ns | -1.3 | 0.01 |
| Psmb9 | Proteasome subunit, beta type 9 | 1.6 | 0.034 | 1.3 | Ns |
| Psmc2 (Rpt1) | Proteasome 26S subunit, ATPase 2 | 1.2 | 0.044 | -1.1 | Ns |
| Psmc4 (Rpt3) | Proteasome 26S subunit, ATPase 4 | 1.2 | 0.02 | -1.3 | Ns |
| Psmc5 (Rpt6) | Proteasome 26S subunit, ATPase 5 | 1.2 | 0.036 | -1.2 | Ns |
| Psmd2 (Rpn1) | Proteasome 26S subunit, non-ATPase, 2 | 1.2 | 0.043 | -1.4 | 0.019 |
| Psmd4 (Rpn10) | Proteasome 26S subunit, non-ATPase, 4 | 1.1 | Ns | -1.3 | 0.014 |
| Psmd7 (Rpn8) | Proteasome 26S subunit, non-ATPase, 7 | 1.2 | 0.013 | 1 | Ns |
| Psmd11 (Rpn6) | Proteasome 26S subunit, non-ATPase, 11 | 1.1 | Ns | -1.3 | 0.021 |
| Psmd14 (Rpn14) | Proteasome 26S subunit, non-ATPase, 14 | 1.3 | 0.012 | -1.1 | Ns |
| Psme4 | Proteasome activator subunit 4 | 1.2 | 0.049 | -1.2 | Ns |
| Ubiquitin-mediated proteolysis | |||||
| Anapc2 | Anaphase promoting complex subunit 2 | 1.3 | 0.004 | -1.1 | Ns |
| Anapc10 | Anaphase promoting complex subunit 10 | 1.3 | 0.038 | -1.1 | Ns |
| Rbx1 | Ring-box 1 | 1.2 | 0.026 | -1.1 | Ns |
| Ube2d1 | Ubiquitin-conjugating enzyme E2D 1 | 1.3 | 0.041 | -1.2 | Ns |
| Ube2d2 | Ubiquitin-conjugating enzyme E2D 2 | 1.2 | 0.033 | 1.1 | Ns |
| Ube2d3 | Ubiquitin-conjugating enzyme E2D 3 | 1.4 | 0.009 | -1.1 | Ns |
| Ube2e2 | Ubiquitin-conjugating enzyme E2E 1 | 1.4 | 0.03 | -1.1 | Ns |
| PPAR signalling | |||||
| Acox2 | Acyl-Coenzyme A oxidase 2, branched chain | -1.2 | Ns | -1.3 | 0.05 |
| Angptl4 | Angiopoietin-like 4 | -1.9 | 0.003 | -2.7 | <0.001 |
| Apoa5 | Apolipoprotein A-V | -1.5 | 0.029 | -1.5 | 0.011 |
| Cyp8b1 | Cytochrome P450, family 8, subfamily b | -1.1 | Ns | -1.6 | 0.016 |
| Dbi | Diazepam binding inhibitor | 1.1 | Ns | -1.2 | 0.016 |
| Fabp1 | Fatty acid binding protein 1, liver | 1.3 | 0.032 | -1.2 | Ns |
| Fabp2 | Fatty acid binding protein 2, intestinal | 1.4 | 0.007 | -1.2 | Ns |
| Hmgcs2 | 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 | 1.2 | Ns | -1.4 | 0.035 |
| Pck1 | Phosphoenolpyruvate carboxykinase 1, cytosolic | -1.6 | 0.007 | -2.2 | <0.001 |
| Pdpk1 | 3-phosphoinositide dependent protein kinase-1 | -1.3 | 0.045 | -1 | Ns |
| Rxrα | Retinoid X receptor alpha | 1.3 | 0.044 | -1.1 | Ns |
| Sorbs1 | Sorbin and SH3 domain containing 1 | 2.2 | <0.001 | -1.7 | Ns |
| Ubc | Ubiquitin C | 1.3 | 0.011 | -1.4 | Ns |
| PPAR signalling, Fatty acid metabolism | |||||
| Acadm | Acetyl-Coenzyme A dehydrogenase, medium chain | 1.1 | Ns | -1.3 | 0.02 |
| Acox1 | Acyl-Coenzyme A oxidase 1, palmitoyl | -1.1 | Ns | -1.4 | 0.035 |
| Cpt2 | Carnitine palmitoyltransferase 2 | -1.1 | Ns | -1.4 | 0.002 |
| Ehhadh | Enoyl-Coenzyme A, hydratase | -1.5 | 0.039 | -2.9 | <0.001 |
| Fatty acid metabolism | |||||
| Acadvl | Acyl-Coenzyme A dehydrogenase, very long chain | -1 | Ns | -1.3 | 0.017 |
| Acat1 | Acetyl-Coenzyme A acetyltransferase 1 | 1.2 | 0.02 | -1.3 | 0.049 |
| Acat2 | Acetyl-Coenzyme A acetyltransferase 2 | 1 | Ns | 1.4 | 0.019 |
| Adh4 | Alcohol dehydrogenase 4 (class II), pi polypeptide | 2.2 | <0.001 | 1.3 | Ns |
| Dci | Dodecenoyl-Coenzyme A delta isomerase | 1 | Ns | -1.3 | 0.012 |
| Hadhb | Hydroxyacyl-Coenzyme A dehydrogenase | 1 | Ns | -1.4 | 0.009 |
| Hsd17b4 | Hydroxysteroid (17-beta) dehydrogenase 4 | 1 | Ns | -1.3 | 0.013 |
| Jak-Stat signalling | |||||
| Ccnd1 | Cyclin D1 | 1.7 | 0.001 | 1.7 | 0.006 |
| Ccnd2 | Cyclin D2 | 1.4 | 0.046 | 1.3 | 0.032 |
| Ghr | Growth hormone receptor | 1.4 | 0.031 | 1.6 | 0.032 |
| Ifnar1 | Interferon (alpha and beta) receptor 1 | 1.2 | 0.005 | 1.2 | Ns |
| Il2rb | Interleukin 2 receptor, beta chain | -1 | Ns | 1.3 | 0.05 |
| Lifr | Leukemia inhibitory factor receptor | 1 | Ns | 1.3 | 0.013 |
| Pik3r1 | Phosphatidylinositol 3-kinase, regulatory subunit | 1.7 | 0.005 | 1.1 | Ns |
| Prlr | Prolactin receptor | 1.5 | Ns | 1.4 | 0.004 |
| Stat5b | Signal transducer and activator of transcription 5B | -1.3 | 0.028 | -1 | Ns |
| Protein_export | |||||
| Hspa5 | Heat shock 70kD protein 5 | 3.2 | <0.001 | 1.8 | Ns |
| Sec61a1 | Sec61 alpha 1 subunit | 1.5 | 0.009 | 1.1 | Ns |
| Sec61b | Sec61 beta subunit | 1.7 | 0.003 | 1.1 | Ns |
| Sec63 | SEC63-like (S. cerevisiae) | 1.5 | 0.007 | 1.1 | Ns |
| Spcs2 | Signal peptidase complex subunit 2 | 1.5 | 0.019 | 1.3 | Ns |
| Spcs3 | Signal peptidase complex subunit 3 | 1.5 | 0.001 | 1.2 | Ns |
| Srp9 | Signal recognition particle 9 | 1.2 | 0.01 | 1 | Ns |
| Srp14 | Signal recognition particle 14 | 1.3 | 0.019 | -1.2 | Ns |
| Srp19 | Signal recognition particle 19 | 1.3 | 0.007 | 1.1 | Ns |
| Srp68 | Signal recognition particle 68 | 1.3 | 0.008 | 1.1 | Ns |
| Srprb | Signal recognition particle receptor, B subunit | 1.4 | 0.02 | 1.5 | Ns |
| Spliceosome | |||||
| Hspa1a | Heat shock protein 1A | 1.8 | <0.001 | 1.1 | Ns |
| Hspa1b | Heat shock protein 1B | 4 | 0.033 | 1.7 | Ns |
| Hspa8 | Heat shock protein 8 | 2.6 | 0.01 | 1 | Ns |
| Lsm6 | LSM6 homolog, U6 small nuclear RNA associated | 1.4 | 0.015 | -1.1 | Ns |
| Pcbp1 | Poly(rC) binding protein 1 | 1.2 | 0.008 | 1.1 | Ns |
| Phf5a | PHD finger protein 5A | 1.3 | 0.012 | -1 | Ns |
| Prpf3 | PRP3 pre-mRNA processing factor 3 homolog (yeast) | 1.3 | 0.01 | 1.1 | Ns |
| Sf3a3 | Splicing factor 3a, subunit 3 | 1.3 | 0.013 | 1.1 | Ns |
| Sf3b5 | Splicing factor 3b, subunit 5 | 1.3 | 0.006 | -1 | Ns |
| Sfrs2 | Splicing factor, arginine/serine-rich 2 (SC-35) | 1.5 | 0.001 | 1.2 | Ns |
| Sfrs3 | Splicing factor, arginine/serine-rich 3 (SRp20) | 1.8 | <0.001 | 1 | Ns |
| Sfrs7 | Splicing factor, arginine/serine-rich 7 | 1.6 | <0.001 | 1.2 | Ns |
| Snrpa | Small nuclear ribonucleoprotein polypeptide A | 1.3 | 0.006 | 1.2 | 0.013 |
| Snrpd1 | Small nuclear ribonucleoprotein D1 | 1.3 | 0.031 | 1.2 | Ns |
| Snrpe | Small nuclear ribonucleoprotein E | 1.2 | 0.041 | 1 | Ns |
| Thoc4 | THO complex 4 | 1.5 | 0.009 | -1.1 | Ns |
| Usp39 | Ubiquitin specific protease 39 | 1.3 | 0.03 | 1.1 | Ns |
| Steroid biosynthesis | |||||
| Fdft1 | Farnesyl diphosphate farnesyl transferase 1 | 2.1 | 0.013 | 2 | 0.008 |
| Fdps | Farnesyl diphosphate synthetase | 1.8 | Ns | 2.5 | 0.029 |
| Ggps1 | Geranylgeranyl diphosphate synthase 1 | 1 | Ns | 1.3 | 0.015 |
| Hmgcr | 3-hydroxy-3-methylglutaryl-Coenzyme A reductase | 1.2 | Ns | 1.9 | 0.024 |
| Idi1 | Isopentenyl-diphosphate delta isomerase | 1.5 | Ns | 2 | 0.018 |
| Lss | Lanosterol synthase | 1.2 | 0.029 | 1.6 | 0.002 |
| Mvd | Mevalonate (diphospho) decarboxylase | 1.2 | Ns | 1.7 | 0.007 |
| Nsdhl | NAD(P) dependent steroid dehydrogenase-like | 1.6 | Ns | 1.4 | 0.035 |
| Sc4mol | Sterol-C4-methyl oxidase-like | 2.4 | Ns | 2.6 | 0.058 |
| Sqle | Squalene epoxidase | 2.8 | Ns | 2.1 | 0.031 |
Only genes in these pathways showing statistically significant (P<0.05) differential expression in response to HFD in at least one strain are reported. Transcription ratio (TR) of genes showing statistically significant downregulation in response to HFD is highlighted in green and TR of significantly upregulated genes is highlighted in red. Ns, not statistically significant. Additional information (Entrez Gene and Affymetrix probeset ID) are in Table S3.