Using the R package (DESeq), the differentially expressed genes (DEGs) were analyzed. 
DESeq
Based on the Cluepedia plug-in in Cytoscape software, enrichment analysis for the protein-coding genes amongst the DEGs was conducted.  Subsequently, protein-protein interaction (PPI) network was built by Cytoscape software. 
Cytoscape software
Using survival package, the genes that could distinguish the survival differences of the HCC samples were explored. 
survival package
Using the R package (DESeq), the differentially expressed genes (DEGs) were analyzed. 
R package