Figure 1

Patterns of DNA methylation across UC methylation subgroups. The methylation levels for subgroup-specific DMRs are shown for 98 UC samples (columns) divided into the four methylation subgroups. The subgroup-specific DMRs (rows) are grouped into patterns 1 to 3. Relative DNA methylation levels are shown as a heat map pseudo-colored blue (unmethylated) to red (methylated). The Lund gene expression subtypes of the UC samples are shown at the top of the heat map. Characteristics of DMRs are shown in five panels to the right of the heatmap: DMR methylation profiles in four normal urothelium samples (Normal); CpG Island (CGI; green); NCEC overlap (GERP; yellow); Lee et al. 2006 Polycomb targets (PCG; red); chromatin states according to Ernst et al. [17] (HMM; 1, ‘Active promoter’; 2, ‘Weak promoter’; 3, ‘Inactive/poised promoter’; 4 to 5, ‘Strong enhancer’; 6 to 7, ‘Weak enhancer’; 8, ‘Insulator’; 9, ‘Transcriptional transition’; 10, ‘Trancriptional elongation’; 11, ‘Weak transcribed’; 12, ‘Polycomb repressed’; 13, ‘Heterochromatin/low signal’; 14 to 15, ‘Repetitive/CNV’).