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Fig. 1 | Genome Biology

Fig. 1

From: Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation

Fig. 1

Population differences in DNA methylation profiles. a Principal component analysis (PCA) of DNA methylation profiles for all 156 individuals. Red and blue circles represent African (AFB) and European (EUB) individuals, respectively. The proportions of variance explained by PC1 and PC2 are indicated. b Genomic location of differentially methylated sites (DMS), for CpG sites hyper-methylated in AFB (red) and in EUB (blue). Odds ratio and 95% confidence intervals are displayed for AFB-DMS and EUB-DMS, comparing their localization in different genomic locations as provided by Illumina (TSS1500, TSS200, 5′UTR, 1stExon, Body, Exon boundaries [ExonBnd], and 3′UTR), and in enhancer and promoter regions specifically detected in monocytes by ChromHMM phase 15 (see refs. [110, 111]). Odds ratios were computed against the general distribution of the 552,141 CpGs of our dataset. c Proportion of DMS that are hyper-methylated either in AFB (red) or in EUB (blue) individuals. The density of β values of one CpG site by category is given as an illustration of the population differences, with red and blue lines representing the methylation density in AFB and EUB, respectively. d Gene Ontology (GO) enrichment analyses of AFB- and EUB-DMS. For both groups, the top-GO categories reaching 5% FDR are shown, together with the number of genes per category and the log10-transformed FDR-adjusted enrichment P values

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