One potential confound in our analysis of ethanol-responsive gene networks regards the experimental design used for microarray studies. Since the BXD strains used for tissue harvesting were also part of a behavioral genetics analysis on ethanol anxiolytic actions (Putman, Wolen and Miles, manuscript in preparation), the animals received mild restraint stress and behavioral testing, in addition to saline or ethanol treatment (see Methods). Use of S-scores to compare saline vs. ethanol-treated animals was calculated to remove the effect of stress from the derived expression patterns since both groups were handled identically. However, we cannot rule out that an interaction between stress and ethanol, rather than just a response to acute ethanol, might contribute to some of the gene networks found in our studies. Regardless, the large overlap between expression patterns derived here for acute ethanol and a published study on basal gene expression correlating with predisposition to ethanol consumption [71], does lend strong support to the argument that the networks discussed here are likely to be important in behavioral responses to ethanol.
