By comparing the signal transduction pathways involved in the identified core GENs, we found that the hepatocarcinogenesis through NAFLD&NASH was induced through DNA methylation of <i>HIST2H2BE</i>, <i>HSPB1</i>, <i>RPL30</i>, and <i>ALDOB</i> and the regulation of miR-21 and miR-122, and the hepatocarcinogenesis through PBC&PSC was induced through DNA methylation of <i>RPL23A</i>, <i>HIST2H2BE</i>, <i>TIMP1</i>, <i>IGF2</i>, <i>RPL30</i>, and <i>ALDOB</i> and the regulation of miR-29a, miR-21, and miR-122.