Fig. 2

Identification of genes showing coordinately changed DNA methylation and gene expression. a Volcano plot and two-dimensional hierarchical clustering of the differential mRNA expression analysis. Vertical dotted lines: fold change ≥2 or ≤2; Horizontal dotted line: the significance cutoff (FDR p-value = 0.05). Two-dimensional hierarchical clustering was performed using 4687 probes corresponding to 3635 genes across all samples (n = 24). b Starburst plot integrating differential DNA methylation and gene expression analyses. Vertical dotted lines: the significance cutoff (FDR p-value = 0.05); Horizontal dotted line: the significance cutoff (FDR p-value = 0.05). Three-dimensional starburst plot of 123 genes, integrating significant changes in DNA methylation (x-axis) and gene expression (y-axis), with a mean twofold or greater change in gene expression (z-axis). Indicated are genes that are hypermethylated and down-regulated in tumors (red); hypomethylated and up-regulated in tumors (blue); hypermethylated and up-regulated in tumors (orange); or hypomethylated and down-regulated in tumors (green). c Gene distribution in CpG islands and promoter region exhibiting hyper-or hypomethylation and up- or down-regulation. d Correlation plots of DNA methylation versus gene expression in tumors and normal tissues for selected genes. x-axis: DNA methylation level (β value), y-axis: mRNA expression level, r: correlation coefficient