Overview of Motif Discovery

Overview of motif discovery and assignment. Motifs were identified by applying a suite of motif discovery programs to the intergenic sequences identified by the binding data. The resulting specificity predictions were filtered for significance and then clustered to yield representative motifs. Conservation-based metrics were used to identify the highest-confidence subset of these motifs. For cases in which multiple significant binding motifs were found for a factor, we used statistical scores or information from specificity databases to choose a single motif for each regulator. A complete description of the method can be found in Supplementary Methods.