Extended Data Fig. 4: ChIP-seq and ChIP-nexus peaks have significantly more consecutive active k-mers, irrespective of how background genomic sequences were defined.
From: Multiple overlapping binding sites determine transcription factor occupancy
(a) Histograms showing the distribution of consecutive active k-mers in peaks (red) for six TFs: HOXD13, NKX2.5, TBX5, and EGR1 (ChIP-seq), and Pho4 and Cbf1 (ChIP-nexus). Background regions were generated by selecting genomic sequences flanking each ChIP peak. Statistical significance was determined by two-sided Wilcoxon rank sum tests. For EGR1, the large effect size resulted in a Pvalue below computational precision. (b) The vast majority of binding sites are detected with high statistical confidence. Across all six TFs, 56–76% of active k-mers are found at FDR < 0.01.
