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).

Elkon et al. Genome Biology 2005 6:R43   doi:10.1186/gb-2005-6-5-r43