Fig. 3: Gene feature enrichment and expression analysis.
From: Edematous severe acute malnutrition is characterized by hypomethylation of DNA
a Gene annotation enrichment analysis for CpG probes within significant differentially methylated clusters (DMCs) from the analysis of acutely malnourished children. P values were calculated with hypergeometric tests of depletion or enrichment comparing N = 420,500 of all tested, background CpG probes with the subset of N = 630 CpG probes found within DMCs. b Intraindividual correlation (Spearman) between mean methylation and mean expression of highly expressed genes within 10 kb in 20 additional Malawian children with SAM at individual CpG probes within significant DMCs. Horizontal dark bars represent median correlation coefficients, dashed line shows correlation of zero, and dotted lines indicate thresholds beyond which correlations reach statistical significance (algorithm AS 89 t test, P < 0.05). 5′UTR: 5-prime untranslated region, TSS1500: within 1500 bp distance to transcription start site, TSS200: within 200 bp distance to transcription start site, 3′UTR: 3-prime untranslated region, IGR: intergenic region. c Beta-value methylation levels by SAM type in DMC overlapping MED24 (left panel, NESAM = 164 samples, NNESAM = 145 samples) next to scatterplots showing the relationship between methylation levels of probes within the MED24 containing DMC and the expression values of MED24 (middle and right panel). Gray dashed lines show a linear model fit, while rho values indicate Spearman correlation coefficients. Source data for panels a and c (density plot) are provided as Source Data file.
