The differentially expressed miRNAs, mir-93, mir-101, mir-182, mir-340, mir-590 and let-7e, and the differentially methylated genes, BMPR1B, CDC25B, DAXX, DDIT3, FOS, JUN, MAP2K4, MAP4K2, MYC, NFKB1, NFKB2, PDGFB, PPP3CA, RAP1A, TAB2, TNFRSF1A and TRAF2, regulate cell proliferation, apoptotic process, cell cycle, cell survival and metastasis through TGF-beta and MAPK pathways in the switch between stage II HCC and stage III HCC. This evidence concerns the gene RAP1A and hepatocellular carcinoma.