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.

Jia et al. BMC Systems Biology 2012 6(Suppl 3):S13   doi:10.1186/1752-0509-6-S3-S13

Open Data