Weighted correlation network analyses (WGCNA, v.1.70-3) [16] were performed to identify modules of co-expressed genes and co-methylated CpG-sites. We assessed the relationship of these modules with AUD case/control status and tested the overlap between associated modules. WGCNA clusters the input matrix according to a dynamic tree-cutting algorithm, using a soft power threshold that approximates the criterion of scale-free topology (Rsigned2 > 0.80). Resulting soft power thresholds for expression networks were 6 for CN, 5 for PUT, and 14 for VS; for methylation networks, all power thresholds were 2.
