We show that HCC are underpinned by the dysregulation of oncogenic processes related to transcriptional and translational control, metabolism, the Wnt-β-catenin, AKT/mTOR and Notch pathways, which are differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels. Here, AKT1 is linked to hepatocellular carcinoma.