. Author manuscript; available in PMC: 2014 Oct 8.

Published in final edited form as: Psychol Med. 2011 Aug 19;42(3):607–616. doi: 10.1017/S0033291711001607

Table 2.

Testing for over-representation of smaller ISC GWAS p-values in hypothesis-driven candidate genes for schizophrenia and genes corresponding to major hypotheses.

Gene list	Boundary ± 0 kb	Boundary ± 10 kb

SZGene hypothesis-driven candidate genes
Full set of genes	0.05	0.02
Full set, excluding MHC region	0.48	0.49
Full set, LD correction (InRich)	0.63	0.19
Genes studied ≥3 times	0.19	0.45
Genes studied ≥3 times, excluding MHC region	0.65	0.52

Genes in DAVID cluster 1 (synaptic transmission)
Full set of 4808 genes	1	1
Subset of 222 hypothesis-driven candidate genes	0.99	1

Genes in DAVID cluster 2 (neuronal development and morphogenesis)
Full set of 4834 genes	1	1
Subset of 401 hypothesis-driven candidate genes	0.73	0.95

Empirical p-values (from ALIGATOR unless otherwise noted) testing for over-representation of smaller ISC GWAS p-values in a given gene list in comparison to that expected by chance (10,000 permutations). SNPs were mapped to strict (±0 kb) or expanded (±10 kb) gene boundaries. SNP thresholds to select the top 5% of genes varied from 0.002 – 0.004.