Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer

Table 3 Parameters and summary of the significant pathways by each pathway analysis method.

Method	Parameter(s)	# pathways (P< 0.01)	# pathways (FDR< 0.2)	The PGDB gene set	Other external gene sets
GenGen	π = 1000	4	3	N	N
ALIGATOR	π = 10,000, P = 0.05	0	0	N	N
SRT	π = 1000, P = 0.05	3	0	N	N
Plink set-based test	π = 1000, r² = 0.5, P = 0.05, max = 5	15	15	Y	N
GSEA	π = 1000	5	7	N	N

This table lists the parameters used in GenGen, ALIGATOR, SRT, the Plink set-based test, and the Gene Set Enrichment Analysis (GSEA). The third and forth columns contain the number of pathways selected by tier one criterion (nominal P < 0.01) and tier two criterion (FDR < 0.2), respectively. The fifth and sixth columns indicate whether the method could identify the PGDB gene set or other additional gene sets (more details available in main text).
π: number of permutations.