In addition, the genes TRAF2, MAP2K4, NFATC2, MAPKAPK2, and CDC25B were differentially methylated and the miRNA let-7a, mir-494, let-7e, and mir-93 were dysregulated during stage II HCC, inducing MAPK pathway perturbation, which in turn resulted in the aberrant regulation of DDIT3, JUN, NFKB1 on their corresponding target genes, ADM, HDAC9, CAPNS1, and CYLD, and subsequent dysfunction in cell proliferation, apoptosis, and cell cycle. This evidence concerns the gene JUN and hepatocellular carcinoma.