Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis

Table 2 Significantly enriched transcription factor binding site signatures in promoters of co-clustered genes

Cluster	Number of genes*	Dependence of gene induction^†			Binding-site enrichment^‡
		ATM	Rel-A (NFκB)	p53	NFκB (M00054)	ATF2 (M00179)
1	26	++	++	+	9.7 (6.0 × 10^-12)	-
3	46	++	-	++	-	2.9 (2.7 × 10^-5)
4	12	+	-	++	-	6.6 (3.6 × 10^-6)

*Number of genes with promoter sequence data. ^†Strong attenuation in induction of the cluster's genes in the respective cells is denoted by ++; partial attenuation is denoted by +; and no attenuation by -. ^‡The ratio between transcription-factor hit prevalence in the cluster and in the background sets of promoters, and its p-value (accession numbers for transcription-factor binding site models are from TRANSFAC DB).