Fig. 2

Coordinated regulation of expression and methylation in MHC region (chr6: 28477797–33448354). a Mapping the 72 regionally significant (q value <0.05) Spearman correlations between site-specific methylation and gene-level expression and b the 100 strongest, regionally significant (q value <0.05), pairwise Spearman correlations between gene expression levels. Mapped according to position on chromosome; green = positive correlation; purple = negative correlation; tan histogram indicates density of genes in region; blue histogram indicated density of CpG loci in region. c Plotting mean methylation and expression level for GDM cases (blue) and matched controls (red) and d the difference in mean methylation and expression between these groups across the MHC region. e Plotting difference in mean methylation and expression between GDM cases and controls across eight random regions to inform appraisal of coordinated regulation across MHC region. The eight regions included the following: chr1:16318931–21396338 (red), chr11:1868700–6913644 (blue), chr12:52616097–57666521 (green), chr14:98919898–103804291 (purple), chr17:35656660–40673466 (orange), chr5:174771462–179709813 (yellow), chr7:97501417–102576358 (brown), and chr9:134394271–139329735 (pink). Methylation level was collapsed across loci within 5 kb, restricting the maximum cluster width to 10 kb. Expression level was plotted at the transcription start site; for the plots of differential expression, gene labels were added for differences >0.10