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We compared the different biological processes and occurrence numbers of gene ontology (GO) in high expression (fold change≥2) activated amelogenin Y-linked (AMELY) non-regulation network of human hepatocellular carcinoma (HCC) and the corresponding low expression activated network of no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection).The biological processes in HCC contained actin filament-based movement, adhesion to symbiont, binding of host cell surface coreceptor, calcium-dependent cell-cell adhesion, cell cycle checkpoint, cytokinesis, DNA damage induced protein phosphorylation, endothelial cell migration, establishment of chromosome localization, induction of apoptosis, intracellular signaling cascade, keratinocyte proliferation, localization within membrane, low density lipoprotein mediated signaling, nucleocytoplasmic transport, protein complex localization,Rac protein signal transduction, Rho protein signal transduction, spindle checkpoint,sprouting angiogenesis, susceptibility to natural killer cell mediated cytotoxicity, viral envelope fusion with host membrane, virion attachment.We proposed and constructed a model of activated AMELY coupling downstream low density, Rac and Rho signal and nucleocytoplasmic transport to cytokinesis, spindle checkpoint and DNA damage protein phosphorylation-induced keratinocyte proliferation network including BIRC5, MAP2K6,CAMK1, CDH13 from activated GO-molecular network of HCC in GEO data set by gene regulatory network inference method and our programming.Our hypothesis was verified by the corresponding activated up-/down-stream network of HCC and inhibited network of no-tumor hepatitis/cirrhotic tissues, no result compared with activated network of no-tumor hepatitis/cirrhotic tissues and inhibited network of HCC.