Fig. 2

Characterization of shared and subtype-specific PMDs. A A representative window of DNA methylation profiles from 45 esophageal samples. Average methylation values are shown in consecutive and non-overlapping 10-kb tiles. CGI regions were masked using the annotation from Irizarry et al. [39]. B Different PMD categories were identified based on the frequency and overlap between the two esophageal cancer types. C Line plots showing average methylation levels for different PMD categories in esophageal tumors, where each line represents one sample. D Similar line plot patterns were observed using TCGA methylation datasets, showing the mean and standard deviation across samples. Each row in the heatmap below shows an individual sample. E Bar plots showing the percentage of WGBS PMDs overlapping with chromatin B compartments, which were predicted using TCGA methylation datasets and analyzed by minfi package. Methylation datasets in D and E are from the TCGA ESCA HM450k arrays, including 91 ESCC and 75 EAC samples. F Somatic mutation rates based on WGS in the indicated studies, calculated separately for each of the WGBS PMD categories. EAC WGS datasets: 276 samples; ESCC WGS datasets: 508 samples