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Fig. 4 | Genome Biology

Fig. 4

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

Fig. 4

Reproducibility of CAF vs. NAF differential analysis across HM450, EPIC and WGBS platforms. a Pie chart indicating number of differentially methylated probes (DMPs) on the EPIC that are present on the HM450 array. b Segmented pie chart showing number of EPIC DMPs that are present on the HM450 and the proportion that are also called as DMPs using HM450 data. c Scatter plot showing strong agreement in the direction and magnitude of the estimated CAF-NAF methylation difference (Δ β-value) on the EPIC vs. HM450 at the EPIC DMPs. d Genomic region densely covered by probes on the EPIC and HM450 arrays shows extensive differential methylation between CAF and NAF samples on both platforms. e Distribution of DMPs across different genome annotation categories: (1) GENCODE19 genes; (2) CpG islands; and (3) regulatory regions defined using ENCODE DNAse hypersensitivity sites and FANTOM5 enhancers. Probes are separated according to whether they are new to EPIC (blue, n = 2408) or common to HM450 and EPIC (purple, n = 2332)

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