Fig. 1
From: Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data
Overview of the CST pipeline. a Given a ChIP-seq sample, primary TF target genes are identified using the TIP algorithm. b For motif discovery, the binding peaks on target gene promoters are first identified using the narrow peaks located in the putative promoters of the TIP-predicted target genes. c For binding motif discovery, the binding peaks on the target genes are selected, and MEME is used to discover primary TF binding motifs. d FIMO is used to locate the primary TF binding motifs in the binding peaks of the primary TF target genes. e Using the binding motifs generated from MEME for all TFs and adding in motifs from the JASPAR database, SpaMo is used to search for binding motifs of potential partner TFs and to analyse their statistical significances based on their spacings. f The resulting predicted TF complexes and their target genes are reported with GO enrichment results. Target genes are stratified into high- and low-confidence groups based on the SpaMo-calculated statistical significance of their TF complex binding motif spacing