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

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

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)
  1. *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).