Despite some of the genes in these modules (e.g. CTNND2, CDH18, CCL20) displaying copy number variation (CNV) in esophageal cancer [19], we verified that the statistics of differential DNAm and mRNA expression for all gene module members were very robust upon adjustment for CNV-status (Additional file 1: Figs. S4, S5), thus demonstrating that CNV is not a confounder. Here, CTNND2 is linked to esophageal cancer.