High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
Figure 5
Enhancer grammar elements deduced from mouse ES cell transcription factor binding sites predicted by GEM.
A) The binding site distribution of Sox2, Klf4, Nanog, Oct4, Esrrb, Nr5a2 and Tcfcp21l in 123 regions that exhibit Sox2-Klf4 spatial binding constraints. The Sox2 sites are aligned at the 0 bp positions, and Klf4 sites are at the 25 bp positions. The rows are ordered by Esrrb offset positions. B) Color chart representation of 201 bp sequences in the same regions as in A. Each row represents a 201 bp bound sequence. Green, blue, yellow and red indicate A, C, G and T. The motif logos are generated by STAMP [19] from the motifs discovered using all the binding sites in the respective datasets.