22Genome-wide association studies on alcohol dependence, by themselves, have yet to account for 23 the estimated heritability of the disorder and provide incomplete mechanistic understanding of 24 this complex trait. Integrating brain ethanol-responsive gene expression networks from model 25 organisms with human genetic data on alcohol dependence could aid in identifying dependence-26 associated genes and functional networks in which they are involved. This study used a 27 modification of the Edge-Weighted Dense Module Searching for genome-wide association 28 studies (EW-dmGWAS) approach to co-analyze whole-genome gene expression data from 29 ethanol-exposed mouse brain tissue, human protein-protein interaction databases and alcohol 30 dependence-related genome-wide association studies. Results revealed novel ethanol-regulated 31 and alcohol dependence-associated gene networks in prefrontal cortex, nucleus accumbens, and 32 ventral tegmental area. Three of these networks were overrepresented with genome-wide 33 association signals from an independent dataset. These networks were significantly 34 overrepresented for gene ontology categories involving several mechanisms, including actin 35 filament-based activity, transcript regulation, Wnt and Syndecan-mediated signaling, and 36 ubiquitination. Together, these studies provide novel insight for brain mechanisms contributing