Activated and repressed enhancers associated with epithelial-mesenchymal transition-related gene clusters (EMT-GCs) and different sets of transcription factors. (A) Box plots of percentile ranks of differential expression for genes associated with each enhancer cluster. Boxes are colored by average magnitude of gain (blue) or loss (red) of enhancer-associated marks. (B) Overlap between gene clusters and genes linked to enhancer clusters. Bubbles are colored with respect to enhancers in the same manner as the boxes in panel A. Size of the bubbles represents the -log10 P value of the overlap. (C) Association of activated and repressed enhancer clusters with transcription factor binding sites. Significance of overlap between ENCODE transcription factor binding sites (columns) and the 10 enhancer clusters with the strongest activated signatures as well as the 10 equivalent repressed enhancer clusters (rows). Each spot on the heat map is the -log10 P value of the overlap, which is Z-score normalized by row. (D) Association of p65 binding sites with gene clusters via enhancers. Enrichment of p65 binding sites (ENCODE) in the enhancers assigned to each gene cluster.