Table 1.

Percent of sets found as significant for the simulated data

	FET
	5.9	9.2	13.8	18.4	GSEA	SUMSQ	SUMSTAT
Pseudo-gene sets
No associated genes	1.4	2.8	0.0	0.9	3.2	3.7	3.7
1-9 weakly associated genes	9.8	3.3	1.6	3.3	8.5	8.2	8.2
10+ weakly associated genes	10.6	7.7	1.9	1.9	11.5	11.5	15.4
1-2 strongly associated genes, but no weakly associated genes	0.0	0.0	5.3	0.0	0.0	0.0	0.0
Real gene sets
Many weakly associated genes	51.7	49.2	13.3	5.0	58.3	60.0	70.8
Some strongly associated genes	2.5	3.8	7.5	33.8	6.3	36.3	23.8
Null sets (no associated genes)	0.0	6.7	1.7	3.3	1.7	5.0	3.3