Based on the DNA methylation data and the paired gene expression data of twelve genes in 371 HCC tissues, functional DNA methylation analyses showed that six genes, including SPP1, RDH16, LAPTM4B, LCAT, CYP2C9 and LECT2, had a significantly strong negative correlation between with gene expression and DNA methylation, and four genes (HMMR, KIF20A, TPX2 and TTK) showed moderate or weak correlation (Fig. 9b, e, Additional file 11: Figure S7), while the methylation data involving ANXA10 and MAGEA6 were lacked. This evidence concerns the gene HMMR and hepatocellular carcinoma.