Differential Methylation Analysis of CD in Blood

We obtained the methylation data from a recent study that conducted differential methylation analysis using 121 CD cases and 191 healthy controls (Ventham et al., 2016 (link)) (GEO accession ID: GSE87648). The study provided whole genome methylation using Illumina HumanMethylation450 BeadChip platform (GPL13534), which contained ∼485,000 probes. We requested the methylation results from the author of the study. This differential methylation genes was generated using whole blood leukocyte samples. In the original work (Ventham et al., 2016 (link)), the authors normalized the methylation matrix using the R package lumi and estimated the cell proportion by the R package minfi. Lastly, Limma was used to identify differentially methylated CpG probes. Probes were mapped to genes according to the annotation file of the chip (Jiang et al., 2016 (link)). For genes with multiple probes, we selected the most significant probe for the gene.