Fig. 2 | Nature Communications

Fig. 2

From: DNA methylation at enhancers identifies distinct breast cancer lineages

Fig. 2

Genomic location of emQTL-CpGs according to ChromHMM and TF binding regions a Bar plot showing the enrichment of emQTL, Cluster 1 and Cluster 2 CpGs over the expected frequency of CpGs from the Illumina HumanMethylation450 across functional/regulatory regions of the genome as determined by MCF7 ChromHMM annotation62. The height of the bars represents the level of enrichment measured as a ratio between the frequency of all emQTL-CpGs (white), CpGs in Cluster 1 (red) and CpGs in Cluster 2 (blue) overlapping a functional element over the expected frequency if such overlaps were to occur at random. Statistically significant enrichments (p < 0.05; hypergeometric test) are marked with an asterisk. b Enrichment analysis of CpGs in Cluster 2 across ERα (white), GATA3 (blue), FOXA1 (red) and CTCF (green) binding regions as determined by ChIP-seq analysis. Enrichment is calculated for different genomic regions determined by MCF7 ChromHMM annotation. For this analysis some ChromHMM annotations were collapsed into one as follow: Enhancer = ‘Enhancer’ and ‘Enhancer + CTCF’ and Promoter = ‘Promoter’, ‘Promoter + CTCF’ and ‘Poised Promoter’. The height of the bars represents the level of enrichment measured as a ratio between the frequencies of CpGs in Cluster 2 in each ChIP-seq peak at specific regulatory region over the expected frequency if such overlaps were to occur at random. Statistically significant (p < 0.05; hypergeometric test) enrichments are marked with an asterisk

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