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Table 1 Functional categories over-represented in clusters of genes similarly regulated by Hfe-disruption in the liver

From: Gene expression profiling of Hfe-/-liver and duodenum in mouse strains with differing susceptibilities to iron loading: identification of transcriptional regulatory targets of Hfe and potential hemochromatosis modifiers

Category Term n EASE score
Cluster 1 (284 Affy IDs [248 genes])
   GOTERM_BP Steroid metabolism 11 1.4 × 10-5
   GOTERM_MF Mono-oxygenase activity 10 3.7 × 10-5
   GOTERM_MF UDP glucuronosyltransferase activity 5 2.9 × 10-2
Cluster 3 (218 Affy IDs [196 genes])
  No functional category overrepresented   
Cluster 4 (145 Affy IDs [139 genes])
   GOTERM_BP Rhythmic process 6 6.5 × 10-5
   KEGG_PATHWAY Fatty acid metabolism 7 3.2 × 10-6
   GOTERM_BP Defense response 14 4.7 × 10-3
   GOTERM_BP Nitrogen compound metabolism 9 5.6 × 10-3
Cluster 5 (94 Affy IDs [84 genes])
   KEGG_PATHWAY Glutathione metabolism 8 5.8 × 10-8
   GOTERM_MF Iron ion binding 8 2.7 × 10-4
Cluster 6 (364 Affy IDs [315 genes])
   SP_PIR_KEYWORDS Fatty acid metabolism 15 2.5 × 10-14
   SP_PIR_KEYWORDS Oxidoreductase 31 1.1 × 10-8
   GOTERM_MF Iron ion binding 19 1.6 × 10-6
   KEGG_PATHWAY Bile acid biosynthesis 6 1.1 × 10-3
   GOTERM_BP Cholesterol metabolism 6 3.2 × 10-3
Cluster 8 (219 Affy IDs [209 genes])
  No functional category overrepresented   
  1. Affymetrix probesets in the different k-means clusters shown in Figure 2 were compared with Affymetrix MG-430 2.0 probe sets for over-representation of gene categories, using the DAVID (Database for Annotation, Visualization, and Integrated Discovery) functional annotation tool. The Category column shows the original database/resource from which the terms originate. The Term column indicates enriched terms associated with the gene list. The n column indicates the number of genes involved in the term. The expression analysis systematic explorer (EASE) score is a modified Fisher exact P value [51]. BP, biological processes; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular functions; PIR, Protein Information Resource; UDP, Uridine 5'-diphospho.