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Figure 2 | Genome Medicine

Figure 2

From: Comparison of DNA methylation profiles in human fetal and adult red blood cell progenitors

Figure 2

Differential DNA methylation between fetal liver- and bone marrow-derived erythroblasts. Volcano plots of differentially methylated (A) CpGs, (B) genes, (C) promoters, and (D) erythroid enhancers. Differentially methylated single CpGs have a difference in DNA methylation β-values between fetal and adult erythroid cells ≥20% and a P ≤1.25 × 10−7. Red and blue points correspond to CpGs significantly hypomethylated in fetal- and adult-stage erythroblasts, respectively. For genes, promoters, and erythroid enhancers, we combined P values from CpG sites that fall within each unit using a generalization of Fisher’s method to take into account correlation of values at nearby sites. For genes, promoters, and enhancers, we averaged the DNA methylation β-values of the CpGs that fall within the unit (y-axis). We used a Bonferonni-adjusted statistical threshold to define differentially methylated functional regions. (E) An enrichment of differentially methylated CpGs was observed in erythroid enhancers when compared to gene or promoter regions also tested on the Illumina HumanMethylation 450 k BeadChip. We used probes that fall outside of these regions to calculate the fold enrichment. (F) Erythroid enhancers (red) are enriched in differentially methylated CpGs when compared to enhancers defined in other cell lines using data from the ENCODE Project.

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