redundant motifs, the top 50 motifs resulting from each search were combined, remapped and ranked according to enrichment (depletion) in the enhancer set. In parallel, we also used HOMER to calculate the enrichment of ChIP-seq derived known transcription factor motifs. Motif collections including search parameters are deposited in a web database at http://enhancer.binf.ku.dk. Histograms of PhastCons scores were generated using the annotation tool in HOMER.
