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

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

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
  1. 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).
  2. π: number of permutations.