Fig. 1
DNA methylation identifies subtype-specific hypermethylation signatures in colon cancer. a Genome-wide methylation profiles measured by HM27K in healthy normal colon mucosa and colon cancer. Multidimensional scaling (MDS) plot includes all probes on the array. b Recursively partitioned mixture model (RPMM)-based unsupervised clustering of colon cancer (n = 55) methylation profiles from panel a. Heatmap shows β-values of CpGs (5254) with SD > 0.16 across all samples (top variable probes). c Volcano plots show differential methylation analysis between nonCIMP- and CIMP-CCs vs. healthy normal colon mucosa (HNM). Colored dots represent significant (P < 0.0001, fold change > 2, β-difference > 10%) hypomethylated (green) or hypermethylated (red). At the top number of significant CpGs and at the bottom number of samples are shown. The x-axis denotes log2 fold changes in methylation relative to HNM and y-axis denotes −log10 of false discovery rate (FDR)-adjusted P value. d Venn diagrams show comparisons of hypermethylated CpGs identified in nonCIMP-CC and CIMP-CCs. e The number of CC-neutral-CpGs (CCN-CpGs) and CIMP-CC-specific CpGs (CIMP-CpGs). f Venn diagram shows comparisons of CCN-CpGs and CIMP-CpGs with previously published sites methylated in CIMP-cancers (GSE25062). g Heatmap shows β-values of CCN-CpGs (1312) and CIMP-CpGs (1800) in eight cancers and paired normal tissues. h Dot plots show methylation difference at CCN-CpGs and CIMP-CpGs between tubular adenoma (TA), sessile serrated adenoma/polyp (SSA/P), nonCIMP-CC, and CIMP-CC from paired normal tissue (dashed line). Black circles show medians. P values were calculated with Wilcoxon rank-sum test. i Bar plot shows number of CCN-CpGs and CIMP-CpGs hypermethylated over age in the HNM (left). P values and odds ratio (OR) were calculated with Fisher's exact test. Density plot shows the rates of methylation change per 10 years of age (right). P values were calculated with Wilcoxon rank-sum test. Methylation rate ratio (MRR); median-rateCCN-CpGs / median-rateCIMP-CpGs. j Density plot shows the difference in the rate of methylation change in HNM from aspirin users (≥ 2 years) or HRT users (after age 50) to nonusers. P values were calculated with Wilcoxon rank-sum test. Methylation rate ratio (MRR); median-rateuser / median-ratenonuser