A detailed description of the methods and analyses concerning microarrays used in this study were previously described [60]. Briefly, custom 8×44 K tilling arrays (Agilent technologies) containing probes selected to tile all the cytokines and TF loci (∼100 Kb) were manufactured by Agilent (Mississauga, Canada). Three replicate microarrays were hybridized and analyzed for each sample. Extracted probe intensities were analyzed using the R software environment for statistical computing [99]. Log-ratios of the bound (Cy5) and input (Cy3) microarray channel intensities were computed for each microarray and then microarrays were normalized to one another using quantile-normalization [100] under the assumption that all samples have identical overall methylation levels.
