Figures 1, 2, 3, 4, S1, S2, S3, S4, S5 and S6 were obtained using the UCSC genome browser (http://genome.ucsc.edu/). They depict whole-chromosome views of tracks composed of average normalized probe intensity differences between groups and Pearson’s correlation coefficient (r) between cytokine levels in plasma and normalized MeDIP microarray probe intensities. Similarly to methylation differences, region-level statistical significance was calculated as enrichment probe correlations close to 1 or −1 among the probes in each 1000 bp region partition of the loci tiled with probes using the Wilcoxon rank-sum test. A probe and the containing region were called correlated with cytokine levels if the p-value of the correlation was at most 0.05 (uncorrected for multiple testing), the absolute value of the coefficient derived from the linear model used to calculate the p-value was at least 0.5 and the false discovery rates (FDR) of the region-level statistic was at most 0.2. Cytokine levels in plasma were obtained from previous work [32] for the same set of individuals from which DNA methylation profiles were derived.
