Fig. 1

Motif enrichment analysis can be based on discrete sets of sequences or scored sequences. a Diagram of inputs to a typical differential ChIP-seq binding experiment, consisting of replicates in stimulated and unstimulated conditions, and an input experiment(s). b Diagram of set-based motif enrichment methods. These methods receive significantly differentially regulated subsets of regulatory sequences (e.g. peaks) and return a significantly enriched subset of TF motifs. c Diagram of score-based motif enrichment methods. These receive a list of scored sequences based on differential signal between stimulated and unstimulated conditions, then return TF motifs enriched towards the top or bottom of the scored sequences. d Illustration of the potential output of a score-based enrichment method, featuring motif name, motif logo, and a description of the enrichment of a motif towards the top or bottom of scored sequences