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Fig. 6 | Genome Biology

Fig. 6

From: Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

Fig. 6

Identification of enhancer sets predicted to be co-regulated by the same transcription factor. a For 38 motifs enriched within hypomethylated probe-gene pairs in one or more cancer types, we calculated the 95 % confidence interval (CI) for the motif enrichment odds ratio; the lower bound of the 95 % CI is shown for each cancer type in the heatmap. b An illustration of the method for linking sets of enhancers with the same motif to an upstream TF regulator (see Methods for additional details). For each of the 38 (m) enriched motifs identified in panel (a), the average DNA methylation at all distal enhancer probes having that motif (in a specific tumor type), was compared to the expression levels of each of 1,777 (k) human TFs (Additional file 17). One such pair is shown as a scatter plot of all breast cancer (BRCA) tumor and adjacent normal samples, for the GATA motif and the GATA3 TF. BRCA samples (660) are color coded by integrated molecular subtypes defined by the TCGA Pan Cancer project, and extremes are selected as the 20% of samples with the lowest methylation (U) and the 20% with the highest methylation (M). A Mann-Whitney U test was performed to obtain the raw P value (p r ). All 1,777 TFs were then ranked by p r (plot at upper right), and the top 5% of the ranked TFs (dashed blue line) were considered to be significantly associated. The top three ranked TFs, along with each member of the specific DNA-binding family (in this case, GATAs) are labeled. Additional file 10 contains ranked TF plots for all motifs and all cancer types. c One of the 230 hypomethylated probe-gene pairs in BRCA containing a GATA motif corresponds to a downstream enhancer of the CCND1 gene. ENCODE ChIP-seq data in the Luminal-subtype MCF7 cell line verify that this enhancer is bound by the ELMER-predicted GATA3 TF

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