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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.

From: How dietary arachidonic- and docosahexaenoic- acid rich oils differentially affect the murine hepatic transcriptome

  Process/Differentiating group(s) FUNG FISH COMB
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