De novo motif discovery from the published ChIP-Seq data (Lodato et al, 2013)

The top de novo sequence motifs (based on enrichment) detected by XXmotif (see Materials and Methods) in ChIP-Seq data for Oct4 in ESCs, Sox2 in ESCs (upper panel), Sox2 in NPCs and Brn2 in NPCs (lower panel). The top 3 enriched motifs for each are shown by the position frequency matrices visualised by WebLogo.