Fig. 3
From: Reduced representative methylome profiling of cell-free DNA for breast cancer detection
Analysis of tumor-related DNA methylation using RRMP. a Heat map shows genome-wide DNA methylation in 100-kb windows across 9 tumor cell lines and 3 WBC samples. Windows are sorted by decreasing DNA methylation for each cell line. Average methylation value for each sample is indicated below. b Heat map depicts hypermethylated and hypomethylated regions in tumor cells compared to WBC samples. c Heat map depicts hypermethylated and hypomethylated regions in each type of tumor cells compared to WBC samples and other tumor cell lines. d, e Heat map depicts 8-kb genomic regions (rows, n = 3972 promoters) centered at transcription start sites and divided into 100 equally sized bins. Panels show average methylation from 1000-cell XRBS profiles for the indicated cell types. Promoters (rows, ≥ 25-fold combined coverage in every cell line) are grouped by the cell line in which they are specifically hypermethylated (d) or hypomethylated (e). Hypomethylated promoters specific to K562 cells are downsampled for visualization. A full list of differentially methylated promoters is provided in Additional file 1: Table S3. f Heat map depicts 8-kb regions (rows, n = 15,202 regions) centered on H3K4me3 peaks identified in NCI-H460 and HT29 ChIP-seq datasets. Rows are ordered by DNA methylation difference between both cell lines. Panels show average methylation from 4-cut RRMP profiles and H3K4me3 signals for NCI-H460 and HT29. Cell-line-specific DNA hypomethylation correlates with H3K4me3 signal. Peaks not specifically hypomethylated in either cell line (‘Others’) were downsampled for visualization