Among genes and proteins that show positive correlation on the CNA-mRNA and mRNA-protein levels and are dysregulated in HCC, we identified candidate driver genes, such as NUDCD1, UBQLN4, BYSL, ATP6V1C1 and RRM2B involved in diverse processes including EMT, cell cycle and DNA damage regulation, and the regulation of the Wnt-β-catenin, AKT/mTOR and Notch pathways. Here, ATP6V1C1 is linked to hepatocellular carcinoma.