Fig. 1

Differential methylation between HCC and normal liver tissues detected by 850K Methylation BeadChip array. A The volcano plot shows 31,937 hypermethylated CpG sites (red) and 216,246 hypomethylated sites (blue). The x-axis represents the DNA methylation differences, while the y-axis represents the p value. B Principle component plot of HCC and normal methylation based on beta value. C Unsupervised hierarchical clustering of the top 1000 methylated CpG sites. The rows represent different CpG sites, and the columns represent different tissue samples. The color in the heatmap represents the methylation beta values. D Hypermethylation locus distribution, whether included in 450K or not. E Venn diagram of the hypermethylation markers identified in this study (n = 840, 450K included), in TCGA-LIHC (n = 1000) and in GSE56588 (n = 1000)