Among the four different class comparison analysis (HCV-related HCC, HCV-related non HCC and Metastatic liver tissue vs. normal control; HCV-related HCC vs. autologous HCV-related non HCC liver tissue) we found a gene-set that distinguish the different cases of liver disease, in particular with time course analysis we identify the genes that should be candidate as a possible progression markers (e.g., GPC3, CXCL12, SPINK1, GLUL, UBD, TM4SF5, DPT, SCD, MAL2, TRIM55, COL4A2). This evidence concerns the gene GPC3 and liver disorder.