Fig. 2
From: Pan-cancer predictions of transcription factors mediating aberrant DNA methylation
TF motif enrichment in hypo-methylated, CpG-poor, distal DMRs. a Pan-cancer motif enrichment. Heatmap of best enriched motifs across all cancer types using a p-value threshold of 10–3 and selecting one motif per TF using the best p-value summed across all cancers. Motif cluster and CpG content are shown. b Pan-cancer TF expression. Heatmap of the expression of corresponding TFs using positive mean FPKM difference between cancer and healthy samples. Motifs highlighted in bold with black squares have matching motif enrichment and TF upregulation. c BRCA motif enrichment. Motif enrichment in BRCA DMRs corresponding to the BRCA column in a. Motif p-values (point color) are computed using an hypergeometric test using the number of regions that have at least a motif compared to the fold enrichment over control regions. Each point represents one of the 4928 motifs used. FOX and GATA clusters are highlighted (including several FOXA1 or GATA3 motif points). d BRCA TF expression. TF expression enrichment in cancer compared to healthy samples (log2 mean FPKM). Each point represents one of the 1048 TFs used colored according to their differential expression p-value. FOX and GATA clusters are highlighted. e Expression of FOXA1 and GATA3 TFs. Dot plot showing all samples FPKM values for FOXA1 and GATA3 in cancer compared to healthy samples corresponding to the mean value shown in d