Enrichment of TF motifs at enhancers in the vicinity of E/R-regulated genes. (A) Enriched TF motifs at putative enhancer regions within 400 kb of the transcription start site (TSS) of E/R-regulated genes are shown (binomial test with FDR < 0.01 and enrichment in >5% of regions). P-value, best-known matching TF motif, and the percentage of regions containing the motif are indicated. The similarity score to known TF motifs is shown in parentheses. (B,C) Enrichment of ChIP peaks nearby (max 400 kb from TSS) all expressed genes (gray) or those that were either down-regulated (blue) or up-regulated (red) by E/R. Horizontal bars show the percentage of genes associated with a ChIP peak containing either the indicated TF motif (in B) or the ETS-RUNX motif (in C). P-value of the hypergeometric test is shown for statistically significant enrichment in the repressed group (P < 0.05). The most prominent ChIP peaks from each data set were used for the analysis. See Supplemental Figure S2 for additional details.
