In order to examine the distribution of effect sizes within the positive gene sets, we plotted the odds-ratios for all of the SNPs selected by the algorithm in the four systems selected by our procedure (Fig 1). Modest to moderate association signals were distributed widely within both gene sets and were not confined to a few markers. To give some sense of the statistical significance of the odds-ratios (ORs) associated with these SNPs, for associations with a randomized phenotype, only 1 in 100 SNPs would have an OR ≥ 1.25 We examined 165 SNPs in the GABA system and 90 in the Glutamate system. Thus, one would expect one or two of the ORs ratios from GABA receptors SNPs to exceed 1.25, whereas we observe nine. For glutamate receptor SNPs, we would expect 1 and we observe 4. For the NE system we would expect to see 0 or 1 SNP whose OR exceeds 1.25; we see three. For the CRH system we expect on average to see one SNP whose OR exceeds 1.2 one half of the time; in fact we see two.
