Factor recognition sites in DNaseI accessible regions are more highly bound in vivo than sites in closed chromatin. Separately for each transcription factor, all significant recognition sequences in the euchromatic genome for four affinity cohorts were identified using PWMs derived from in vitro DNA binding data (Table 1) [17,70]. In addition, matches to ten PWMs derived by random permutation of nucleotide position order were derived for each factor. Sites in each affinity cohort for both the genuine and scrambled PWMs present were each classified as either accessible or inaccessible, using the 5% FDR DNaseI accessible regions to define accessible regions (Table 1). The median ChIP-chip scores (y-axis) for the 500-bp regions ±250 bp around recognition sites in each affinity cohort were plotted separately for accessible (red lines) and inaccessible (blue lines) genomic regions. Dark red and blue lines show results for the genuine factor PWMs, light red and blue lines the median result for the scrambled PWMs. The highest affinity cohort is to the left (x-axis). Web logo representations of the PWM representing the highest and lowest affinity cohorts of genuine recognition sites are shown at the bottom. The 95% confidence limits for the median ChIP-chip scores are indicated. Plots for (a) CAD, (b) GT, (c) KNI, and (d) HRY are shown. Additional file 8 provides similar plots for all 16 factors for which sufficiently accurate PWMs are available.
Li et al. Genome Biology 2011 12:R34 doi:10.1186/gb-2011-12-4-r34