Table 1 |
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|
Functional categories over-represented in clusters of genes similarly regulated by Hfe-disruption in the liver |
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| Category |
Term |
n |
EASE score |
|
|
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| Cluster 1 (284 Affy IDs [248 genes]) |
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| 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]) |
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| No functional category overrepresented |
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| Cluster 4 (145 Affy IDs [139 genes]) |
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| 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]) |
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| 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]) |
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| 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]) |
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| No functional category overrepresented |
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|
|
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|
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. |
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Coppin et al. Genome Biology 2007 8:R221 doi:10.1186/gb-2007-8-10-r221 |
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