Fig. 4

Hypermethylation of gene-body but not promoter within canyon is associated with increased gene expression. a DNA methylation of upregulated and downregulated pan-cancer hypermethylated canyon genes between a uterine tumor (Data ID: TCGA-AX-A1CI-01A) and its matched normal sample (TCGA-AX-A1CI-11A). b Increased methylation in gene-body and low methylation around TSS for HOXB13. c Gene expression and DNA methylation in HOXB13 promoter (chr17: 46,806,000-46,807,000) and gene-body (chr17:46,802,200-46,805,999) between uterine normal (22) and tumor (427) samples. P values were calculated by Wilcoxon signed-rank test. d Correlation between HOXB13 expression and methylation level at gene promoter (left) and gene-body (right) in uterine normal (22) and tumor (427) samples. The rho and p value were computed by Spearman’s rank test. e Locus-specific spearman’s rank correlation of gene expression change and DNA methylation change (see “Methods”) between a uterine tumor and its matched normal sample in Fig. 4a for pan-cancer hypermethylated canyon genes (left), pan-cancer hypermethylated cUMR genes (middle), and all differentially expressed genes (right)