Figure 3

Analysis of the three TCGA datasets. The top panel (A-C) shows results of CpG site-level analysis and the bottom panel (D-F) shows results of the CpG island-level analysis. Plot (A) shows the numbers of significantly differentially methylated CpG sites for the three cancer datasets; (B) shows the numbers of significantly differentially variable CpG sites for the three cancer datasets; (C) shows the overlap of the top differentially methylated and top differentially variable CpG sites for each cancer dataset separately. The dotted line shows the median overlap profile of two sets of 10,000 randomly selected CpGs. The random sampling was repeated 1000 times. Plot (D) shows the numbers of significant differentially methylated CpG islands; (E) the numbers of significant differentially variable CpG islands; and (F) shows a proportional venn diagram of the overlap of the top differentially variable CpG islands between the three different cancers.