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As a complex disease, the development and progression of hepatocellular carcinoma (HCC) involves the interactions of multiple proteins, genes and miRNAs in various biological pathways, and it has been extensively studied with different high-throughput techniques. However, efforts to integrate multiple data sources at different levels, especially with regard to biological pathways and interaction networks, are still negligible in the HCC research field. We have built a database of the HCC network (HCCNet) by integrating interactions of multiple proteins, genes and miRNAs in biological pathways, and manually collecting all of the HCC-related genes and miRNAs from the literature in combination with a bioinformatic analysis of the collected HCC expression data (Supplementary information, Data S1). Currently, there are 37 811 experimentally confirmed protein-protein interactions (PPIs), 9 148 experimentally …