Table 2.

Enriched TF PWMs in Promoters of Genes That Function in the Cell Cycle

Biological process category	Number of genes	TF	Analytical score	Rank relative to abundance in random sets
Cell cycle control	223	ETF	1.5 × 10−7	1
(GO 000074)		E2F	1.5 × 10−6	1
		NRF-1	2.5 × 10−5	1
		Sp1	2.5 × 10−4	4 (2)
Mitotic cell cycle	175	E2F	1.4 × 10−9	1
(GO 0000278)		NF-Y	1.3 × 10−4	1 (2)
		NRF-1	1.6 × 10−4	1
DNA metabolism	240	E2F	6.7 × 10−5	1
(GO 0006259)		NF-Y	4.6 × 10−4	4 (2)
		Sp1	6.8 × 10−4	5 (5)
M phase	100	NRF-1	5.9 × 10−6	1
(GO 0000279)		NF-Y	2.5 × 10−4	2 (2)
		ATF	3.4 × 10−4	4 (5)
		E2F	3.8 × 10−4	1

Promoters in the 13K set were assigned to functional categories. Functional annotations of genes were extracted from LocusLink DB, which uses the GO vocabulary (Maglott et al. 2000). Four categories related to the cell cycle, containing a total of 672 distinct genes, were analyzed (certain genes are assigned to several categories; hence the categories are not mutually exclusive). The number of promoters and the TF PWMs significantly enriched in each category are indicated. Indicated for each overrepresented PWM are the analytical score for observing such enrichment and the rank of the PWM's abundance in the functional category relative to its abundance in 10,000 sets of randomly selected promoters of the same size as that of the functional category set. Numbers in parentheses represent the number of random sets in which the PWM was equally abundant as in the functional category set.