Networks were constructed using following settings: minimum module size = 30, mergeCutHeight = 0.25, maxBlockSize = 36,000. In WGCNA, modules are labeled using colors. In the “Results” section modules are labeled according to type of data, brain region, and color assigned in the analysis, e.g., “e-VS-pink” for module “pink” from the WGCNA analysis of gene expression data in the ventral striatum. For each module, its eigengene was calculated and correlated with AUD status. Association of modules with AUD status and covariates is shown in Supplementary Fig. 4. For modules associated with AUD status, we performed enrichment analysis using the GOenrichmentAnalysis function implemented in the WGCNA package for expression data and the R package missMethyl (v.1.20.4) [35] for methylation modules. Further, we extracted hub genes of AUD-associated WGCNA expression modules by calculating the product of module membership and gene significance for each gene of a module. Based on this score, the 10% of highest-ranking genes were defined as module hub genes. To investigate the biological relevance of hub genes, protein-protein interaction networks were generated using the Search Tool for the Retrieval
