To identify and compare motif signatures characterizing facet-specific enhancers (permissive set) we applied de novo motif analyses. Motif enrichment was analyzed using HOMER. Enhancer regions (400bp) were compared to ~50,000 randomly selected genomic fragments of the same region size, as described above. Twenty-five motifs were searched for a range of motif lengths (7-14 bp) resulting in a set of 200 de novo motifs per set, which was further filtered to remove redundant motifs. In parallel, we also used HOMER to calculate the enrichment of ChIP-Seq derived motifs. Motif collections including search parameters for all facets are deposited in the web database at http://enhancer.binf.ku.dk. Known transcription factor motifs were used to compare motif enrichment between facets.
