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Fig. 6 | Genome Biology

Fig. 6

From: Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

Fig. 6

Ability of EPIC to detect differential methylation at distal regulatory elements defined using ENCODE DNAse hypersensitivity data. a, b Scatter plot showing overall agreement in DNA methylation between EPIC probes and WGBS across distal regulatory regions for (a) PrEC and (b) LNCaP. cf. Comparison of DNA methylation between EPIC and WGBS across distal regulatory regions. Tracks show ENCODE DHS data across 177 reference cell lines and PrEC and LNCaP DHS data separately; EPIC and WGBS methylation measurements for PrEC and LNCaP; and WGBS coverage for each site, with the 10X threshold represented by a dashed purple line for reference. Dark grey shading indicates regions that were not assayed by each technology. c Genomic region shows agreement in DNA methylation between EPIC probe and WGBS across distal regulatory region re13.110396155. PrEC features a DNAse sensitive peak and low methylation, while LNCaP lacks DNAse sensitivity and has high methylation. d Genomic region shows agreement in DNA methylation between EPIC probe and WGBS across distal regulatory region re22.41658115. LNCaP features a DNAse sensitive peak and low methylation, while PrEC lacks DNAse sensitivity and has high methylation. e Genomic region shows disagreement in DNA methylation between EPIC probe and WGBS across distal regulatory region re2.153430015 due to probe positioning. PrEC features a DNAse sensitive peak and high methylation at the border of the peak where the EPIC probe is located, but low methylation in the centre of the peak (not covered by EPIC probes). f Genomic region shows disagreement in DNA methylation between EPIC probe and WGBS, in both LNCaP and PrEC samples, across distal regulatory region re6.28654415

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