Analysis of whole brain gene expression in two replicate lines of mice selectively bred for high and low ethanol preference (HAP/LAP) identified 249 differentially expressed transcripts [39]. A list of eight candidate genes was generated based on their inclusion both in an expression quantitative trait locus (eQTL), as determined by global gene expression levels in BXD recombinant inbred strains, and in a behavioral quantitative trait locus (bQTL) for ethanol preference, as previously published [76, 77]. Only two of these genes, however, had expression levels correlated with ethanol intake in BXD recombinant inbred strains. Further analysis of the candidate gene promoters identified 23 over-represented transcription factor binding sites. Among those, binding motifs for Foxk2 and Tcf1 were present in the promoter of seven of the eight candidate genes, while Nfkb1 and Smad3 were localized within bQTL for ethanol preference. None of these transcription factors, however, were differentially expressed between HAP and LAP mice. A meta-analysis of whole brain gene expression in three groups of mouse lines selected for high and low ethanol intake (High Short-Term Selection [STS]/Low STS mice which were
