Analysis of ChIP-Seq data and its intersection with transcriptional profiling data.

<p>(A) Distribution of ChIP-seq peaks highlighted the modeled GLI3-binding centered in peak regions, using MACS2 software. (B) GLI3 ChIP-seq revealed 1316 peaks defining potential binding sites in the mouse genome. Intersection with <i>shh</i>-dependent transcriptional profiling identified 112 candidate direct Hedgehog-dependent target genes. (C) Summary of <i>de novo</i> and known motifs enriched in <i>shh</i>-dependent GLI3-bound regions (Top 2 sub-panels) compared with similar known GLI motifs from literature and TRANSFAC database (Bottom 3 sub-panels). (D) Among the 112 genes, 26 are transcription factors or regulators of transcription, a significant over-representation. (E) Among the 112 genes, 4 are FOX family transcription factors, a significant over-representation.