Characterization of DNA methylation in COX-2-induced HCC of TG mice. (a) The methylation levels of 3717 DMRs (1.25-fold change and false discovery rate <5%) in three HCC vs three livers (w/o HCC) and from different TG mice are shown in a heat map (the blue, green and yellow colors represent lower than average, close to average and higher than average methylation level, respectively). Unsupervised hierarchical clustering analysis was applied. (b) DNA methylation patterns in different genomic regions, including upstream, 5’-UTR, promoter, coding sequence (CDS), 3’-UTR, intron and downstream. (c) Scatter plot of 695 DMRs at promoter region in three HCC vs three livers (w/o HCC) from different TG mice. The data are represented by median with interquartile range. (d) Enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis for 3717 DMRs and 1742 DEGs. Pathways with 10 or more genes involved and a P-value <1e-06 are considered as significantly affected. Gene number involved in different pathway is indicated above bars.