To find genes regulated by exposure to ethanol, we determined the time course of gene expression changes from immediately following a just sedating ethanol exposure to 3.5 hours later, when accumulated ethanol has been completely metabolized and expression of ethanol rapid tolerance is high (Scholz et al., 2000). This approach has 2 main benefits over single time-point sampling used in previous studies of ethanol regulation of gene expression: assumptions about sampling time are minimized, and small but temporally consistent changes in gene expression can be detected. For example, we detected the coordinate up-regulation of immunity genes that was largely missed previously (Fig. S2). Moreover, we sampled gene expression in whole fly heads that included the entire brain (excluding the thoracic ganglion), trachea, fat bodies, and musculature. Regional effects of ethanol exposure on gene expression could result in relatively small alterations in overall expression levels that are nonetheless critical for the behavioral actions of ethanol. We detected gene expression changes that overlapped with those identified in 2 previous studies of the effects of ethanol exposure in Drosophila (Morozova et al., 2006;
