Expression patterns in normal tissues explain differential susceptibility to hypermethylation in cancer. (a) Consistently hypermethylated genes are more tissue specific than variably hypermethylated genes. Shown are histograms of tissue-specificity scores (as Figure 2b) observed at hypermethylation prone genes that were consistently or variably methylated in different tumor types. Differences between gene sets were tested using Wilcoxon rank sum tests (*** P < 0.001, ** P < 0.01 and * P < 0.05). (b) Variably hypermethylated genes with differential susceptibility in breast cancer are differentially expressed in normal breast tissue. Shown are boxplots of the relative level of expression in different cells from normal breast found at VM genes that are either frequently or never hypermethylated in breast tumors . Differences between cellular fractions were tested using Wilcoxon rank sum tests. Lum = luminal epithelial cells, Lum Pro = luminal progenitor cells, Bas = basal myoepithelial cells, Stroma = breast stromal cells. (c) Variably hypermethylated genes that are prone to hypermethylation in tumors are repressed in the corresponding normal tissue. Shown are boxplots of the expression levels measured for VM genes with different susceptibility in individual tumor types in the corresponding normal tissues. Res = never hypermethylated in tumors, Prone = frequently hypermethylated in tumors. Differences between gene groups were tested using Wilcoxon rank sum tests. (d) Repressed genes are more prone to hypermethylation than active genes in colorectal cancer. Shown are heatmaps of the methylation levels of CGI promoter genes that are unmethylated in normal colon tissue and are either activated (left) or repressed (right) in normal colon as compared to normal liver. The 356 repressed genes are methylated to a significantly higher level than the 1,465 active genes (one-sided Wilcoxon rank sum test P = 1.6x10-7). CGI, CpG island; VM, variably methylated.