Table 5.

Enrichment of the biological process categories from Gene Ontology (GO)

Pair ID	Motif or motif pair	GO biological process	Total no. of genes with the term	Total no. of target genes with the term	Enrichment	P-value
—	HNF-1	Regulation of blood pressure	28	3	15.2	0.001
		Regulation of body fluids	79	4	7.2	0.002
		Response to pathogenic bacteria	13	2	21.8	0.004
		Cytolysis	14	2	20.2	0.004
		Blood coagulation	64	3	6.6	0.01
		Hemostasis	69	3	6.2	0.01
P1	TGACCTTTG*HNF-1	Hexose metabolism	98	5	4.7	0.004
		Monosaccharide metabolism	101	5	4.6	0.005
		Muscle development	105	5	4.4	0.006
		Inflammatory response	153	6	3.6	0.006
		Fructose metabolism	13	2	14.1	0.008
		Energy derivation by oxidation of organic compounds	118	5	3.9	0.009
		Main pathways of carbohydrate metabolism	76	4	4.8	0.009
P3	ARP-1*ATGGAAAGA	Lipid transport	57	4	6.7	0.003
		Lipoprotein metabolism	31	3	9.2	0.004
		Inflammatory response	153	6	3.7	0.005
		Glycosphingolipid metabolism	15	2	12.6	0.01
		Response to wounding	235	7	2.8	0.01
P2	TGACCTTTG*ACCCTAGACC	Response to external stimulus	556	48	1.7	0.0003
		Response to pest, pathogen or parasite	385	35	1.8	0.0008
		Response to wounding	235	24	2.0	0.001

Significant GO terms with P⩽0.01 (q⩽0.15; Storey and Tibshirani, 2003) are reported here. Enrichment (column 6) quantifies how enriched a given category is with the target genes (Zeeberg et al, 2003). P-value was calculated using a hypergeometric distribution (see Materials and methods). Parent terms with higher P-values than their child terms are not reported in this table. Terms with exactly one gene in the total and target gene sets are also not reported. Some of the P-values are close to the cutoff possibly because the terms are quite broad.