Additional technical factors to be considered in these studies regards the use of only a single microarray per strain/treatment group and the possibility of SNPs affecting microarray probe performance. Although arrays were derived from pooling tissue across 4–5 animals, technical variance could have influenced our results. We believe that such variance would have likely only degraded expression correlations and done so partially given the number of strains used for the genetic correlation analysis. In particular, identification of overlapping trans-eQTL for many genes within a given paraclique (Figs. 5 and S6) is strong evidence for the technical rigor of these studies since such genetic correlations would have been severely affected by technical variance. Regarding potential SNPs affecting hybridization results, this issue was discussed in Methods and a complete list of SNPs identified in probes is included in Table S8. Since our analysis largely focused on ethanol-regulated gene expression and the S-score analysis would cancel out any SNP effect (since both control and ethanol treated samples would be affected), we chose not to eliminate SNP containing probes from our analysis but did penalize them during candidate gene ranking (see Methods).
