Briefly, this integrated analysis of genomewide DNA methylation and gene expression data identified a group of novel gene signatures (ALX3, B4GALNT1, CTHRC1, DLX5, EMX1, IRX3, OTX1, SIX2, TLX1, VASH2, ZIC2, ZIC4, ZIC5, and ZNF695), which may be regulated by DNA methylation in HCC. This evidence concerns the gene IRX3 and hepatocellular carcinoma.