Table 3.

Overview of pathway or network-based GWAS of alcohol-related behaviors

Author, Date	Sample	Phenotype	Analysis tool/method	Gene sets	Summary of key enrichment domains
Kendler et al. (2011)	Molecular Genetics of Schizophrenia control sample	Factor score derived from alcohol craving, DSM-IV alcohol abuse and dependence	ALIGATOR	KEGG, GO	Response to hormone stimulus, membrane raft organization, anatomical structure homeostasis, phosphorylation, and regulation of transporter activity; lipid catabolic processes, regulation of protein transport, regulation of cell adhesion, and cholesterol metabolic process
Kos et al. (2013)	SAGE	DSM-IV alcohol dependence	Permuted Fisher’s exact tests	ResNet Mammalian v. 7.0 database curated by Ariadne Genomics	Maf transcription factors, Hox AbdB genes, chloride transport, glycine and serine metabolism
Biernacka et al. (2013)	SAGE	DSM-IV alcohol dependence	Permutation-based self-contained SNP or gene set analysis	KEGG	Synthesis and degradation of ketone bodies; neuroactive ligand-receptor interaction
Han et al. (2013)	Discovery: COGA+SAGE; Replication: Yale-Penn, OZ-ALC	DSM-IV alcohol dependence	R-package dmGWAS	Protein-protein interaction network, GO	cation transport, synaptic transmission, and transmission of nerve impulses
Juraeva et al. (2015)	Discovery: German sample; replication: COGA, SAGE	DSM-IV alcohol dependence	R-package globaltest version 5.12.0	KEGG, GO, BioCarta, microRNA targets, transcription factor targets, positional gene-sets	Nineteen gene-sets identified in discovery sample, five of which were nominally significant in replication sample, including DNA integration, focal adhesion, leucocyte transendothelial migration, chr7q32, and MIR-377
Adkins et al. (2015)	GSMS, CHDS, VTSABD	Longitudinal alcohol consumption	Hypergeometric test	ConsensusPathDB	Neuronal system, Transmission across chemical Synapses, pharmacodynamics, Adherens junctions interactions, G protein signaling pathways, Axon guidance