Fig. 2
From: Pan-urologic cancer genomic subtypes that transcend tissue of origin
Genomic subtypes of urologic cancers in TCGA cohort by analysis of multiple data platforms. a Integration of subtype classifications from five “omic” data platforms identified nine major groups of urologic cancers being represented in TCGA (n = 1954 cases, including bladder, renal clear cell, renal chromophobe, renal papillary, prostate, and testicular cancers). The heat map displays the subtypes defined independently by DNA methylation (pink), Chromosomal copy alteration (black), mRNA expression (red), microRNA expression (blue), and protein (RPPA) expression (green); each row in this heat map denotes membership within a specific subtype defined by the indicated platform. Data points are colored according to pan-urologic subtype (Table 1). b Differential gene expression patterns (values normalized within each main cancer type), representing a set of genes that help to distinguish between the nine subtypes (for each subtype, showing the top 100 genes most differentially in the given subtype vs. the rest of the tumors). c DNA methylation patterns, with heat map representing the top 2000 genomic loci with the highest variability in DNA methylation patterns across tumors (using a data set with methylation values being normalized within each main cancer type), and with corresponding p16 silencing and CDKN2A copy loss indicated, along with a plot of total DNA methylation index values (fraction of methylation probes with beta>0.3) for each sample. d By TCGA project and genomic subtype (where projects were highly represented within a given subtype), total DNA methylation index values. Box plots represent 5%, 25%, 50%, 75%, and 95%. P-values by Mann-Whitney U-test. See also Supplementary Fig. 2 and Supplementary Data 1 through 4
