Fig. 1

Identification of DNA copy-number-correlated (CNVcor) and DNA methylation-correlated (METcor) genes in HCC. a Distribution of the correlation coefficients between the mRNA expression levels and DNA copy numbers or DNA methylation across the samples are shown, respectively. b A Venn diagram shows the counts of CNVcor and METcor genes. The counts of overlapped genes between CNVcor and METcor are indicated. c Proportional frequencies of the CNVcor or METcor genes against total gene counts in each chromosome arm are shown, respectively. d Genomic positions of DNA methylation probes are categorized based on the positional relations with CpG islands (right) and genes (left), respectively. The proportional frequencies in each category of DNA methylation for the whole genes and METcor genes are compared, respectively. e A barplot shows the frequencies of up- or down-expressed CNVcor genes or METcor genes in each sample (top). Each of CNVcor and METcor genes is categorized as upregulated (CNVcor_UP and METcor_UP) or downregulated (CNVcor_DOWN and METcor_DOWN) genes, respectively. Heatmaps show the up- (red) and down-expressed (blue) CNVcor (middle) and METcor (bottom) genes, respectively. f Dot plots show the pairwise correlations among the frequencies of CNVcor_UP, CNVcor_DOWN, METcor_UP, and METcor_DOWN genes, respectively