Table 3.
Various biofunctions and pathways were altered in the rat liver by the FCE diet compared with control.
| Category | P value | Gene | Upregulated genes | Downregulated genes |
|---|---|---|---|---|
| Biofunctionsa | ||||
| Lipid metabolism | 1.55E − 13 | 83 | 42 | 41 |
| Small molecule biochemistry | 1.55E − 13 | 103 | 55 | 48 |
| Vitamin and mineral metabolism | 9.80E − 13 | 34 | 18 | 16 |
| Drug metabolism | 2.88E − 10 | 26 | 21 | 5 |
| Molecular transport | 5.96E − 07 | 64 | 34 | 30 |
| Nucleic acid metabolism | 1.29E − 06 | 16 | 6 | 10 |
| Carbohydrate metabolism | 1.55E − 04 | 39 | 17 | 22 |
| Cell death | 1.57E − 04 | 21 | 19 | 2 |
| Amino acid metabolism | 7.70E − 04 | 17 | 15 | 2 |
| Cell cycle | 1.21E − 03 | 10 | 7 | 3 |
| Cellular assembly and organization | 1.21E − 03 | 9 | 2 | 7 |
| Gene expression | 1.21E − 03 | 15 | 11 | 4 |
| Cellular function and maintenance | 1.31E − 03 | 7 | 6 | 1 |
| Cellular compromise | 3.54E − 03 | 9 | 6 | 3 |
| Cellular growth and proliferation | 4.16E − 03 | 4 | 3 | 1 |
| Cell-to-cell signaling and interaction | 6.91E − 03 | 7 | 4 | 3 |
| KEGG pathwaysb | ||||
| Polyunsaturated fatty acid biosynthesis | 5.95E − 06 | 7 | 0 | 7 |
| Metabolism of xenobiotics by cytochrome P450 | 7.81E − 06 | 12 | 12 | 0 |
| Biosynthesis of steroids | 8.09E − 05 | 7 | 0 | 7 |
| C21-steroid hormone metabolism | 2.79E − 04 | 5 | 3 | 2 |
| Androgen and estrogen metabolism | 3.08E − 04 | 9 | 6 | 3 |
| PPAR signaling pathway | 1.92E − 03 | 9 | 1 | 8 |
| Linoleic acid metabolism | 3.14E − 03 | 6 | 6 | 0 |
| Alanine and aspartate metabolism | 3.61E − 03 | 6 | 3 | 3 |
| Maturity onset diabetes of the young | 7.55E − 03 | 5 | 0 | 5 |
| Pyruvate metabolism | 1.03E − 02 | 6 | 1 | 4 |
| Bile acid biosynthesis | 2.68E − 02 | 5 | 4 | 1 |
| Glutathione metabolism | 3.48E − 02 | 5 | 4 | 1 |
| Carbon fixation | 3.56E − 02 | 4 | 1 | 3 |
| Nitrogen metabolism | 3.56E − 02 | 4 | 2 | 2 |
We compared the effect of the FCE diet on hepatic gene expression with that of control by using oligonucleotide microarray.
aDifferentially expressed gens list from microarray experiment was imported in Ingenuity pathway analysis, filtered by selecting only genes expressed in rat liver. Significance values expressed as P values were calculated using a right-tailed Fisher's exact test. Biofunctions that were significantly changed were determined.
bWe conducted KEGG pathway analysis by importing a list of differentially expressed genes in DAVID (database for annotation, visualization, and integrated discovery). Significance values expressed as P values were calculated using a modified Fisher exact probability test (EASE score).