The results of our study include the depiction of refined and delineated biological pathways differentially modulated in HCC that is built around TP53, p38 MAPK, ERK/MAPK, PI3K/Akt, NF-κB, TGF-β, MYC, and ERbB-2, including their target genes that were not previously implicated with early HCC. Here, TP53 is linked to hepatocellular carcinoma.