Fig. 5

Integration of gene expression, histone modification, and RE methylation data in PTPRN2 and SDK1. a, b TCGA data reveal positive correlations between the methylation of each CpG in the differentially methylated LINE-1s (dmLINE-1s) and the expression levels of their proximal genes, PTPRN2 and SDK1 (one color represents one CpG). Minimum p values of the correlation across the CpGs in dmLINE-1s are shown. c, h Using the subset of our UFSH samples, the same two dmLINE-1s proximal to genes were hypomethylated (c, d, each dot represents a CpG site in the LINE-1 loci). Repressive H3K27me3 marks were largely gained in both genes in HCC-HCV samples (e, f). Consistently, both genes were downregulated in HCV-HCC compared to normal liver samples (g, h). For each gene, average expression levels between the two selected samples are shown