Figure 3

Complex pattern of DNA methylation in oral squamous cell carcinoma (OSCC) samples. (A) Bar plots of numbers and ratios of hypermethylated and hypomethylated CpGs grouped by gene features. The gene features colored in cold tunes were divided into regions 200 bp upstream of transcriptional start site (TSS200), 1500 bp upstream of TSS (TSS1500), 5′-untranslated regions (5′-UTR), 3′-UTR, the first exon (1st exon), and gene body and intergenic regions (IGR). (B) Bar plots of numbers and ratios of hypermethylated and hypomethylated CpGs grouped by gene and CpG island (CGI) features. The CGI features were divided according to the distance to CGI, including island, shore (regions within 2 kb upstream or downstream of island), shelf (regions of 2–4 kb upstream or downstream of island), and open sea (regions outside of island, shore, and shelf). (C) Plots of the median methylation values per 100 bp distance grouped by gene expression quartiles based on the expression levels in either tumor or normal samples (n = 5493, 5493, 5493, and 5496 for Q1, Q2, Q3, and Q4, respectively; Q4 is the highest expression) showing methylation ratio at 100 bp segments including genomic loci within and outside CpG islands in genes with promoter associated CpG islands. The curves were colored in red in OSCC samples and in blue in normal samples.