Fig. 3

Validation of molecular subtypes using an independent TCGA data. a Overall distributions of correlation coefficients of between the mRNA expression levels and DNA copy numbers or DNA methylation are shown, respectively. b A Venn diagram shows the counts of the DNA coy number-correlated genes (CNVcor) and the DNA methylation-correlated genes (METcor) genes. The counts of the overlapped genes between CNVcor and METcor are indicated. c Proportion of the CNVcor or METcor genes against total count of genes in each chromosome arm are shown. d Composition of DNA methylation probes in the whole genes and METcor genes are compared. Genomic positions of DNA methylation probes are categorized based on the relations with CpG island regions (right) and gene regions (left), respectively. e A plot shows the correlation between the frequencies of CNVcor and METcor genes in each sample. f A heatmap shows the expression patterns of the differentially expressed genes among the subtypes identified by iClusterPlus analysis (top). The frequencies of CNVcor_UP, CNVcor_DOWN, METcor_UP, and METcor_DOWN genes are shown (bottom). g Violin plots indicate the frequencies of CNVcor_UP, CNVcor_DOWN, METcor_UP, and METcor_DOWN genes are shown in each subtype of C1, C2, and C3, respectively. h Kaplan–Meier plot analyses of the HCC subtypes for overall survival (OS) and recurrence-free survival (RFS) are shown, respectively