Figure 3: Cell-type specificity of DNA methylation signals. | Nature Communications

Figure 3: Cell-type specificity of DNA methylation signals.

From: Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease

Figure 3

(a) Principal component analysis demonstrating the first two components of the entire (i) DNA methylation data set (ii) Gene expression data set. Both demonstrate tight clustering according to the cell type of origin of the sample. (b) Volcano plots for IBD versus controls differential methylation position (DMP) analysis for separated cells (CD4+, CD8+ T cells and CD14+ monocytes). (c,d) Boxplots show the median, 25th and 75th percentiles, and 1.5 * interquartile range (error bars) of methylation (beta) values. Cell-specific DNA methylation profiles. (c) The top differentially methylated position (RPS6KA2) was hypomethylated in whole blood and also monocytes. There was a larger difference between cases and controls in the separated cells compared with whole tissue (blood). (d) demonstrates monocyte specific DNA methylation at the histone deacetylase 4 (HDAC4) locus. Beta differences and uncorrected P values derived from linear models (IBD cases versus controls, including age and sex as covariates).

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