Table 2. Results for gene-based test and dynamic module search of three schizophrenia GWAS datasets.

GWAS datasets		MGS	Affy6	Affy500K
No. of genes	Total genes	27,188	26,899	23,420
	Genes in PPI	11,456	11,362	10,232
	Genes in PPI and P-value < 0.05	651 (5.7%)	681 (6.0%)	589 (5.8%)
	Genes in PPI and FDR < 0.6	56 (0.49%)	6 (0.05%)	46 (0.45%)
No. of modules	Initial dmGWAS modules	10,910	10,786	9,481
	① evaluation, P(Z m) < 0.05	786	123	612
	② evaluation in Affy6, P(Z m(eval)) < 0.05	17	-	41
	③ evaluation in Affy500K, P(Z m(eval)) < 0.05	11	19	-
	④ evaluation in MGS, P(Z m(eval)) < 0.05	-	34	5
	Final modules: ①∩(②∪③∪④)	27	6	46
Involved genes (238)		68	29	146
Genes with P-value < 0.05		34 (50%)	17 (58.6%)	83 (56.8%)
Genes with FDR < 0.6		9 (13.24%)	6 (20.69%)	15 (10.27%)