Figure 2

Pan-cancer clustering of TCGA tumors based on DNA methylation levels. Heat maps show levels of DNA methylation for TCGA tumor and control samples. Samples were pooled together across 14 cancer types (all except THCA). Each row corresponds to a sample and each column corresponds to a probe. Color bars show the CIMP status and the cancer type associated to each sample. (A) Heat map showing results for CIMP+, CIMPi, CIMP−, and control samples over a reference pan-cancer set of 8,492 probes (obtained as the union of type-specific sets of differentially methylated probes). Rows and columns were ordered using hierarchical correlational clustering. (B) Same as panel (A), but rows and columns were ranked in decreasing order of average methylation, from top to bottom and from left to right, respectively. (C) Same as panel (B), but average levels of methylation were computed using our proposed panel of 89 pan-cancer differentially methylated loci. In panels (A) and (B), a third color bar shows the relative ranking of each sample in terms of average methylation, with black showing the most methylated sample and white showing the least methylated sample. In panel (C), CIMPi tumors were excluded to facilitate visual comparison of the CIMP+/− categories and, for probes associated to known genes, the actual gene or genes are included next to each probe identifier.