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

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

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

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.

ISSN: 1474-760X