The DNA methylation datasets generated from Illumina HM450K array, EPIC array platform and WGBS were downloaded from the Encyclopedia of DNA Elements (ENCODE) project and GEO Datasets Database (see Additional file 1 ). We processed the HM450K and RPIC data using the ‘minfi’ Bioconductor package [19 (link)]. Probes were excluded if the detection p-value greater than 0.05. The target CpG sites annotated to the sex chromosomes or common SNPs were removed from subsequent analysis. The methylation level of each site was measured as beta-value which was the ratio of signal compared with the sum of the methylated and unmethylated probes.
The WGBS data of H1-hESC and GM12878 cell lines were performed in two biological replicates. First, we merged the two sets of methylation data by summing the read counts. At each CpG site the methylation level was calculated as the ratio of the counts of methylated reads to total reads. Then MethylSeekR was used to identify the UMRs (unmethylated regions), LMRs (low-methylated regions) and PMDs (partially methylated domains) on the WGBS datasets. The other genomic regions were treated as FMRs. The Pearson correlation coefficients of methylation level between WGBS and HM450K datasets for two cell lines and between EPIC and WGBS datasets for GM12878 cell line were calculated on the common CpG sites for different platform.
The WGBS data of H1-hESC and GM12878 cell lines were performed in two biological replicates. First, we merged the two sets of methylation data by summing the read counts. At each CpG site the methylation level was calculated as the ratio of the counts of methylated reads to total reads. Then MethylSeekR was used to identify the UMRs (unmethylated regions), LMRs (low-methylated regions) and PMDs (partially methylated domains) on the WGBS datasets. The other genomic regions were treated as FMRs. The Pearson correlation coefficients of methylation level between WGBS and HM450K datasets for two cell lines and between EPIC and WGBS datasets for GM12878 cell line were calculated on the common CpG sites for different platform.