Following the computational analyses of HCC-relevant gene network topologies, we used quantitative RT-PCR in a cohort of normal liver tissue (elevated transaminases but without underlying liver disease or structural changes of the tissue, n = 8), HCV-induced chronic liver disease (n = 9), and HCC (n = 7) to identify transcripts and validate co-expressions of five well-connected genes, namely ASPM (node degree = 6), CDKN3 (node degree = 21), NEK2 (node degree = 14), RACGAP1 (node degree = 11), and TOP2A (node degree = 31) in the ‘Cell cycle’ cluster of Conserved-Net. This evidence concerns the gene NEK2 and hepatocellular carcinoma.