Fig. 4.

a Network for transcription factor NFKB1 and its inhibitor NFKBIE. Gray circles indicate target CpGs, and arrows represent directed associations (i.e., association between GI and DNA methylation levels). Blue lines indicate a positive association between gene expression and DNA methylation levels; red lines indicate a negative association between gene expression levels and DNA methylation levels. b NLRC5 (chromosome 16) was associated with decreased DNA methylation levels at multiple (N = 43) CpG sites in the classical and extended MHC region (chromosome 6). Red lines indicate a negative association between NLRC5 expression levels and DNA methylation levels. The numbers displayed in the lines indicate how many target CpGs the line represents. Gene labels are displayed if one or more target CpGs were associated with the expression of these genes. Blue gene symbols refer to genes negatively correlated with target CpG methylation (implying upregulation by NLRC5), and vice versa for red labels. Asterisks indicate that the GI corresponding to NLRC5 was also (positively) associated with this gene