Table 2 Genes differentiating FUNG, FISH, and COMB, using gene ontology classifications and enrichment analysis. Genes differentiating FUNG, FISH, and COMB, using gene ontology (GO) classifications and enrichment analysis. Differentially regulated genes (GEA model) were subjected to enrichment analysis to select GO terms "enriched with" these genes. Two broad GO categories included are "Biological Process" and "Molecular Function". Specific GO terms are included and specific genes within each gene term differentiating the diets are parenthesized, alphabetized, and separated by commas. Rows are sorted for consistency with Table 3 where possible. Differentiating genes were selected at P < 0.001, and GO terms computed at P < 0.01; P is the probability a random gene for each GO term will have as many genes with the same GO term as the actual list. The biological process category "Metabolism" was excluded as it was too general. Genes in Tables 2-3 are not identical because of the different statistical approaches utilized. Enrichment analysis placed acadm (acetyl-Coenzyme A dehydrogenase, medium chain (MCAD) in both the FA oxidation and Electron transport categories; it was removed from the latter.

Biological process classifications

Amino acid metabolism

agxt, alas2, bcat1, oat

Acetyl-CoA biosynthesis

acas2, acly

acas2, acly

Fatty acid and lipid synthesis

elovl2, elovl3, fasn, scd1

Fatty acid oxidation

acadm, cpt1a, cpt2

acox1, cpt2, ech1

cpt1a, cpt2, acsl1(facl2)

Carbohydrate metabolism

foxa3, gck

Electron transport (Cyt P450 metabolism)

por, cyp2a4, cyp2b9, cyp3a11, cyp3a16, cyp3a41, cyp4a10

Lipid transport

apoa4, apoc2, osbpl5, pltp

Heme biosynthesis

alad, alas1, alas2

Oxygen transport

hba-a1, hbb-b1

Peroxidase reaction

gpx1, mpo, prdx2

Response to heat, stress, inflammation

hspa8, hspcb, hspb1, hspb8

Molecular function classifications

Structural constituent of cytoskeleton

acta1, acta2, krt1-13, tuba1, tubb2, tubb3, tubb5

Transaminase

agxt, bcat1, oat

Lyase

acly, fasn, pck1, umps

Transferase, transferring groups other than amino-acyl groups

elovl2, lce-pending

Acyltransferase

alas1, alas2, cpt1a, cpt2, fasn, gpam

alas1, alas2, cpt1a, cpt2, fasn, gpam

Monooxygenase/P450

cyp2a4, cyp2b9, cyp3a11, cyp3a41, cyp3a16, cyp4a10

5-aminolevulinate synthase

alas1, alas2

alas1, alas2

alas1, alas2

Oxygen transporter

hba-a1, hbb-b1

Oxidoreductase

acadm, aldh1a1, cyp2a4, cyp2b9, cyp3a11, cyp3a16, cyp3a41, cyp4a10, dct, fasn, gpx1, por, sdh1

Heat shock protein

cryac, hspa8, hspb1, hspcb

Acetate-coa ligase

acas2, facl2

Aspartic-type endopeptidase

ctse, mela

RAS small monomeric gtpase

hras1, rras

Aldehyde dehydrogenase NAD⁺

aldh1a1, aldh1a7, aldh2

Antioxidant

prdx2, prdx4

Hormone

gh, igf2, prlpe, sct

Peptide hormone

igf2, npy, sct

Cathepsin S, L, K

ctsl, ctss

Globin

hba-a1, hbb-b1

Hydroxymethylglutaryl-CoA synthase

hmgcs1, hmgcs2