Enrichment of bound motifs for a given TF and its subfamily members.

<p>All TF ChIP-seq experiments from the Myers-lab released as part of the ENCODE project were downloaded. For each TF ChIP-seq experiment we also obtained the corresponding TF motif from the HOCOMOCO database [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005311#pcbi.1005311.ref025" target="_blank">25</a>]. For a given ChIP-seq experiment, we looked at the processed DHS peaks in the same cell line. We partitioned DHS peaks into two groups depending on whether they were bound by the TF (overlap with a ChIP-seq peak) or not. We then calculated both the fraction of bound and unbound DHS peaks containing a given motif. The enrichment of bound motifs was defined as the ratio of these two fractions. Results are shown from left to right for: the motifs of the TFs that were assayed in the corresponding ChIP-seq experiments (Correct TF motifs), motifs of other TFs from the same subfamily (TF subfamily motifs), and randomly sampled motifs (Random motifs). During sampling, each motif was sampled as often as the number of ChiP-seq experiment available for that motif. We see strong enrichment of TF motifs in ChIP-seq peaks of the TF as well as its subfamily members.