Figure 4

Defining the TFBS zone of enrichment around the peakMax. (a) A visual depiction of the enrichment zone determined with a heuristic procedure, as described in methods. The x-axis presents the upper limit of each 5 bp bin, and the bins are the absolute distance of a motif from the peakMax. The y-axis shows the proportion of peaks from the dataset with a motif in a 5 bp bin. The horizontal green line is fit to the distal background bins, and the horizontal line in blue is the allowance line (see methods). The blue vertical dashed line indicates where the proportion of peaks in a non-background bin approaches the allowance line without falling below it – this line is the heuristic distance threshold for motif enrichment around the peakMax. (b) The NFYB sequence logo and the TFBS-landscape view for NFYB motifs in NFYB ChIP-Seq data. The heuristic enrichment zone is between the blue vertical dashed lines. The black vertical lines indicate the beginning of the distal background region (spanning 200-500 bp from the peakMax). (c) The width of the motif enrichment zone (y-axis) for human ChIP-Seq datasets (x-axis); multiple datasets for a TF were averaged to obtain one enrichment zone value per TF. Vertical bars are the average differences between all of the enrichment zone widths for a TF. The red horizontal line is the mean. (d) The proportion of peaks within the enrichment zone for a TF’s set of ChIP-Seq datasets were averaged. The x-axis provides, for each of 85 TFs, the mean proportion of peaks with a motif scoring above the motif score threshold and located within the zone of enrichment (mean 0.60, median 0.61).