Among them, 3 lncRNAs (GBAP1, MCM3AP-AS1, and SLC16A1-AS1) (Figure 4A–4C, 4G–4I), 15 mRNAs (ACLY, BAX, BIRC5, CDC6, CDCA5, CHEK1, FOXM1, ITGA2, LAMC1, MCM5, MYB, PAK1, PRKAA2, SOX4, and TK1) (Supplementary Figures 5Aa–5Ao, 6Aa–6Ao) and 3 miRNAs (hsa-miR-10b-5p, hsa-miR-183-5p, and hsa-miR-222-3p) (Supplementary Figures 5Aa–Ao, 6Ba–Bc) were identified as pro-tumor factors because of their high expression in cancer tissues and their correlation with shorter OS in patients with HCC. Here, SOX4 is linked to hepatocellular carcinoma.