The aim of this exploratory study was to detect both overlapping and specific changes in gene expression in cocaine addicts and alcoholics. Therefore we based our analysis for each gene on the plots shown in Figures 1, 2 and 3. For example, in Figure 1 it can be seen that GAD1 and GAD2 have lower expression in cocaine addicts compared with both alcoholics and controls. As indicated in Table 2, the predominant analyses were: cocaine addicts vs. alcoholics+controls (7 analyses) (specific effect); cocaine addicts+alcoholics vs. controls (7 analyses) (overlapping effects); alcoholics vs. cocaine addicts+controls (4 analyses) (specific effect) and cocaine addicts vs. alcoholics (4 analyses) (specific effect). P values were corrected in the analyses in humans and in the analyses in P/NP rats using the False Discovery Rate (FDR) [28] based on 25 candidate genes. Global P values were calculated using the truncated product method [29], a modified Fisher's method (ftp://statgen.ncsu.edu/pub/zaykin/tpm). P values from all 25 independent tests with P<0.05 were combined and global significance was assessed by evaluating the distribution of their product.
