This indicated that FAM99A‐ and FAM99B‐related DEGs and DE‐miRNAs may be participating in mediating processes such as cell cycle, apoptosis, metastasis, immunity, inflammation, ECM remodeling and metabolic reprogramming, which further confirmed the regulation of these phenotypes by FAM99A and FAM99B in HCC. This evidence concerns the gene FAM99A and hepatocellular carcinoma.