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Fig. 5 | Genome Biology

Fig. 5

From: Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

Fig. 5

Relationship between DNA methylation and gene expression. a The proportion of cell type-specific HVPs that map to gene promoters and are positively (red), negatively (blue), or not (white) associated with gene expression levels at Benjamini–Hochberg-corrected P < 0.05 (Spearman’s rank correlation). We found that around one-third of these HVPs (30.1%; range 23.5–33.3%) are negatively correlated with gene expression. b Same as panel a but for HVPs that map to gene bodies. c The negative correlation of MSR1 promoter DNA methylation with gene expression in monocytes (r = −0.70, P < 2.2 × 10−16; Spearman’s rank correlation). d Correlation between DNA methylation variability (MV) and gene expression variability at gene promoters in neutrophils. First, gene-wise MV values were calculated. Then, the values were ordered from low to high MV value, grouped together in bins of 100 genes, and plotted against the EV values, maintaining the ordering by MV values. This binning strategy was applied to reduce the complexity of the data. HVPs at gene promoters were defined as CpG sites annotated to TSS1500, TSS200, 5′ UTR, and first exon, according to the Illumina 450 K array annotation manifest. Darker data points indicate the subset of bins that is further discussed in the “Results” section. e Same as panel d but for HVPs that map to gene bodies. HVPs at gene bodies were defined as CpGs annotated to body and 3′ UTR, according to the 450 K array annotation manifest. f The number of consensus transcription factor (TF) binding motifs at promoter regions versus MV values in neutrophils. Promoter regions were defined as ±500 bp around the transcription start site. Darker data points indicate the subset of bins that is further discussed in the “Results” section

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