Fig. 3

Epigenetic relationships among normal kidney and LTS/STS ccRCC groups. a Phyloepigenetic tree derived using 4100 DMCpG shared between the normal kidney samples and the STS/LTS groups. b Boxplot comparing the intra-LTS and intra-STS Euclidian distances. Each dot represents the Euclidian distance between any two samples in the group. In the LTS group there are 231 connections, and in the STS group there are 91 connections. c Heatmap showing 12/3207 hypermethylated CpGs in cohort 1 significantly associated with survival and significantly correlated with expression of their respective gene, derived from a. d Heatmap showing 4/893 hypomethylated CpGs in cohort 1 significantly associated with survival and significantly correlated with the expression of their respective gene derived from a. The red color in the heatmap represents a positive correlation between the methylation status of the CpG and expression of the respective gene. The blue color in the heatmap represents a negative correlation between methylation status of the CpG and expression level of its respective gene. The color bar next to the dendrogram indicates the genomic feature where each site in located: body (blue), promoter (red). The information on the opposite side of the dendrogram indicates the methylation status linked to longer patient survival (hyper or hypo) for the CpG in KIRC, the GC number of each CpG, and the respective gene name as per Illumina 450K manifest. CpGs in red text are associated with better survival when hypermethylated. CpGs in blue text are associated with better patient survival if hypomethylated