Fig. 3

Canyon hypermethylation is associated with increased expression of homeobox oncogenes. a DAVID functional annotation of pan-cancer hypermethylated, hypomethylated, and conserved canyons/cUMRs. The p values were adjusted by the BH method. b Oncogene or tumor suppressor [31] gene enrichment levels in the pan-cancer hypermethylated/hypomethylated canyon/cUMRs. P values were computed by Fisher’s exact test. c Venn diagram showing the overlap between pan-cancer canyon hypermethylated homeobox genes (m-homeobox genes) and oncogenes. P value was computed by Fisher’s exact test. d Boxplots showing mean gene expression distribution of five categories gene sets of pan-cancer hypermethylated/hypomethylated canyons/cUMRs associated genes and all genes in the uterine tumor (427) and normal (22) samples. P values were calculated by Wilcoxon signed-rank test. Boxplots represent the interquartile range (25–75%), with the median; whiskers correspond to 1.5 times the interquartile range. e Mean gene expression distribution of the m-homeobox genes and the other homeobox genes between uterine tumors (427) and normal (22) samples. The average expression of each gene was first computed across 22 normal samples or 427 tumor samples. The boxplot shows the average expression of all genes