Core tip: Hepatocellular carcinoma (HCC) is the second cause of cancer-related mortality. The importance of having an early detecting biomarker is to allow for curative measures to be applicable, and prognostic biomarkers to detect survival, in dealing with the disease. In silico analyses allow us to discover new genetic and epigenetic biomarkers, along with establishing the coexpression patterns, which impact HCC survival. Also, it allows for understanding the molecular pathways for HCC pathogenesis, and the discovery of potential therapeutic options. In this article, I review the current discoveries and limitations that face researchers to reach their ultimate goal of establishing clinical practice guidelines. I give an overview of the future potential that could benefit integrated research on HCC and discuss my own research related to the topic.