Skip to main content
Figure 3 | Genome Biology

Figure 3

From: DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML

Figure 3

Relationship between DNA methylation and gene expression in untreated cells. (a) A plot of methylation across composite genes, grouped into deciles by level of expression in untreated cells. Along the gene, DNA sequence is split into windows, each representing 2% of the total gene body, with 10 additional 1 kb windows both up- and downstream of the gene. The y-axis shows the mean percentage methylation for each decile and window. (b) Heatmap of percentage methylated CpGs over genes. Genes are split into windows as (a) and rank ordered according to the expression level of the corresponding transcript (y-axis, increasing expression at top). The intensity of the heatmap indicates the percentage methylation from 0% to 100%, white to red. (c) Heatmap of observed-to-expected CpG ratio in a 10 kb window centered on TSS. Genes are rank ordered as (b). The intensity of the heatmap indicates the value of observed-to-expected CpG ratio from 0 to 1, white to blue. (d) Proportion of CpG islands that are methylated (>80% methylation), partially methylated (20% to 80% methylated) and unmethylated (<80% methylated). (e) Histogram of expression at genes with methylated (>80% methylation), partially methylated (20% to 80% methylated) and unmethylated (<80% methylated) CpG island within 10 kb of the TSS.

Back to article page