A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

Table 3 Discovered cis-regulatory clusters for Arabidopsis

d-clust	d-count	related 6-mers	Functional Cluster Name	f-count	P-val
Fig. 6a	95	AATCGC, ATCGCC, CCGACG, CCGATT, CCTCTC, CGATTT, CGCCGA, CTCCGA, CTCTCC, GACTGT, GCCGAC, TCCGAT, TCGCCG, TCTCCG	cysteine-type peptidase activity	8	4.60E-11
Fig. 6b	50	ACACGT, ACGTGT, CACGTG, CGTGTC	response to water deprivation	11	1.50E-11
			response to abscisic acid stimulus	12	7.90E-11
			PP2C SIG	8	9.80E-11
			Protein phosphatase 2C	8	1.20E-10
Fig. 6c	61	CATGCA	nutrient reservoir activity	12	1.80E-18
			Seed storage protein	7	6.50E-16
Fig. 6d	66	GGCCCA	cytosolic ribosome	64	1.90E-103
			cytosolic part	61	3.10E-99
			ribosomal protein	65	3.00E-121
			structural constituent of ribosome	65	8.10E-104
Fig. 6e	47	CAACGG	cell cycle	11	7.60E-13
			cell division	10	2.00E-12
Fig. 6f	17	GCACGT	plant-type cell wall organization	8	9.80E-14
			Extensin-like region	6	7.00E-13
			structural constituent of cell wall	6	4.40E-11

'd-clust' is the identifier for the discovered clusters; 'd-count' is the number of genes in the discovered cluster; 'f-count' is the number of genes in the functional clusters, which was discovered by previous well-organized experiments; 'P-value' is measured by Fisher's exact test p-value, which measures the enrichment level of the functions within the discovered cis-regulatory cluster relative to the genome.