Methylation profiling of genes with altered expression. (A) Venn diagram illustrating the overlap of genes with hypomethylated or hypermethylated promoters and hypermethylated or hypomethylated gene bodies. (B) Boxplot showing the expression distributions of genes with different methylation patterns. From left to right, green indicates all genes; light red, 9618 genes with hypomethylated promoters; light blue, 71 genes with hypermethylated promoters; dark red, 33 genes with hypomethylated gene bodies; gray, 159 genes with hypermethylated gene bodies; and yellow, 133 genes with both hypomethylated promoters and hypomethylated gene bodies. *Indicates the Student t test P value when comparing each set vs the set with hypermethylated promoters (light blue). (C) Venn diagram shows the overlap of genes with hypomethylated or hypermethylated promoters and genes that were differentially expressed. (D) Boxplots of the β value distributions of all genes promoters (light blue), upregulated promoters (green), and downregulated promoters (red). The hypomethylated (β ≥ 0.2) region is highlighted by red shading. *The Student t test P value, determining the significance of the difference between up/downregulated promoter β values. Down, gene expression is downregulated in ET vs HVP; Up, gene expression is upregulated in ET vs HV; P hyper, promoter hypermethylated; P hypo, promoter hypomethylated.