Figure 6: miR-29 regulation of DNA-demethylation factors TET1 and TDG.

(a) Association between the three miR-29 family members and predicted target genes TET1 and TDG across cancer types. Cancer types are color coded as in Figure 1a, and REC scores are listed for each pair. (b) Relationship between miR-29a expression and TET1 and TDG expression in tumor and representative normal samples in four different cancer types. (c) Global association between TDG expression and gene promoter hypomethylation. In each cancer type, we computed the fraction of gene promoters that were hypomethylated with TDG overexpression among the top 100 promoters showing strongest correlation (Spearman) of DNA methylation and TDG mRNA expression. The average fraction of TDG-associated hypomethylated gene promoters across all cancer types was compared with an empirical null distribution computed from 1,000 sample permutations of the DNA methylation data set in each cancer type.