TABLE 6.
Hepatic gene expression pathways (genes ranked highest to lowest by percentage difference) affected in male mice fed a 45%-fat diet with or without HAMRS2 supplementation for 10 wk1
| Mean, FPKMs |
||||
| Pathway2 | Definition | Control | HAMRS2 | Percentage difference (HAMRS2 relative to control)3 |
| Metabolism of xenobiotics by cytochrome P450 (KEGG pathway: 00980) (C = 77; O = 3; E = 0.08; R = 35.78; rawP = 8.50 × 10−5; adjP = 0.0003) | ||||
| Cyp2b9 | Cytochrome P450, family 2, subfamily b, polypeptide 9 | 3.2 | 9.6 | 204 |
| Cyp2c37 | Cytochrome P450, family 2, subfamily c, polypeptide 37 | 66.0 | 93.9 | 42 |
| Cyp2c54 | Cytochrome P450, family 2, subfamily c, polypeptide 54 | 103 | 133 | 29 |
| Jak-STAT signaling pathway (KEGG pathway: 04630) (C = 153; O = 5; E = 0.17; R = 30.01; rawP = 7.52 × 10−7; adjP = 1.35 × 10−5) | ||||
| Spry4 | Sprouty homolog 4 (Drosophila) | 2.2 | 2.9 | 32 |
| Il6ra | IL-6 receptor, α | 9.7 | 7.4 | −24 |
| Crebbp | CREB binding protein | 3.9 | 2.9 | −27 |
| Cish | Cytokine inducible SH2-containing protein | 16.8 | 9.9 | −41 |
| Myc | Myelocytomatosis oncogene | 4.4 | 2.2 | −50 |
| TGF-β signaling pathway (KEGG pathway: 04350) (C = 85; O = 4; E = 0.09; R = 43.22; rawP = 2.42 × 10−6; adjP = 1.37 × 10−5) | ||||
| Rock1 | Rho-associated coiled-coil containing protein kinase 1 | 12.5 | 9.5 | −24 |
| Crebbp | CREB binding protein | 3.9 | 2.9 | −27 |
| Inhba | Inhibin β-A | 2.4 | 1.5 | −39 |
| Myc | Myelocytomatosis oncogene | 4.4 | 2.2 | −50 |
| Wnt signaling pathway (KEGG pathway: 04310) (C = 154; O = 3; E = 0.17; R = 17.89; rawP = 0.0007; adjP = 0.0014) | ||||
| Rock1 | Rho-associated coiled-coil containing protein kinase 1 | 12.5 | 9.5 | −24 |
| Crebbp | CREB binding protein | 3.9 | 2.9 | −27 |
| Myc | Myelocytomatosis oncogene | 4.4 | 2.2 | −50 |
| Vascular smooth muscle contraction (KEGG pathway: 04270) (C = 123; O = 3; E = 0.13; R = 22.40; rawP = 0.0003; adjP = 0.0007) | ||||
| Cyp4a10 | Cytochrome P450, family 4, subfamily a, polypeptide 10 | 189 | 245 | 30 |
| Rock1 | Rho-associated coiled-coil containing protein kinase 1 | 12.5 | 9.5 | −24 |
| Ppp1r12a | Protein phosphatase 1, regulatory (inhibitor) subunit 12A | 5.7 | 4.1 | −27 |
| Arachidonic acid metabolism (KEGG pathway: 00590) (C = 90; O = 4; E = 0.10; R = 40.82; rawP = 3.04 × 10−6; adjP = 1.37 × 10−5) | ||||
| Cyp2b9 | Cytochrome P450, family 2, subfamily b, polypeptide 9 | 3.2 | 9.6 | 204 |
| Cyp2c37 | Cytochrome P450, family 2. subfamily c, polypeptide 37 | 66.0 | 93.9 | 42 |
| Cyp4a10 | Cytochrome P450, family 4, subfamily a, polypeptide 10 | 189 | 245 | 30 |
| Cyp2c54 | Cytochrome P450, family 2, subfamily c, polypeptide 54 | 103 | 133 | 29 |
| Retinol metabolism (KEGG pathway: 00830) (C = 77; O = 4; E = 0.08; R = 47.71; rawP = 1.63 × 10−6; adjP = 1.37 × 10−5) | ||||
| Cyp2b9 | Cytochrome P450, family 2, subfamily b, polypeptide 9 | 3.2 | 9.6 | 204 |
| Cyp2c37 | Cytochrome P450, family 2. subfamily c, polypeptide 37 | 66.0 | 93.9 | 42 |
| Cyp4a10 | Cytochrome P450, family 4, subfamily a, polypeptide 10 | 189 | 245 | 30 |
| Cyp2c54 | Cytochrome P450, family 2, subfamily c, polypeptide 54 | 103 | 133 | 29 |
| Biosynthesis of unsaturated FAs (KEGG pathway: 01040) (C = 25; O = 2; E = 0.03; R = 73.47; rawP = 0.0003; adjP = 0.0007) | ||||
| Acot3 | Acyl-CoA thioesterase 3 | 9.0 | 13.2 | 47 |
| Elovl6 | ELOVL family member 6, elongation of long-chain FAs (yeast) | 15.5 | 12.1 | −22 |
| Linoleic acid metabolism (KEGG pathway: 00591) (C = 46; O = 2; E = 0.05; R = 39.93; rawP = 0.0012; adjP = 0.0022) | ||||
| Cyp2c37 | Cytochrome P450, family 2. subfamily c, polypeptide 37 | 66.0 | 93.9 | 42 |
| Cyp2c54 | Cytochrome P450, family 2, subfamily c, polypeptide 54 | 103 | 133 | 29 |
Pathways are derived from liver transcriptomics data. Parameters—organism: mus musculus; ID type: gene_symbol; reference set: mmusculus_genome; statistic: hypergeometric; significance level: Top10; multiple test correction: Benjamini-Hochberg; minimum number of genes for a category: 2. Genes included have an adjusted P value ≤ 0.05. adjP, P value adjusted by the multiple test adjustment; FPKM, fragment per kilobase of transcript per million; HAMRS2, high-amylose-maize resistant starch type 2; KEGG, Kyoto Encyclopedia of Genes and Genomes; rawP, P value from hypergeometric test.
The C, O, E, and R in parentheses indicate the number of reference genes in the category, number of genes in the gene set and also in the category, the expected number in the category, and the ratio of enrichment, respectively.
Percentage difference = [(HAMRS2 − control)/control] × 100.