Table 2.

Validation and comparison to other methods in a p53 benchmark microarray dataset

	GSOA			GSEA			GAGE			GSAA
Canonical gene sets	Rank	P	FDR	Rank	P	FDR	Rank	P	FDR	Rank	P	FDR
P53 pathway	1	0.001	0.037	1	0.000	0.009	26	0.093	0.822	1	0.000	0.566
P53 signaling	15	0.002	0.058	21	0.028	0.614	30	0.109	0.822	29	0.048	0.695
P53 hypoxia pathway	1	0.001	0.037	1	0.000	0.009	27	0.103	0.822	5	0.002	0.713
P53 up	1	0.001	0.037	1	0.000	0.065	20	0.083	0.822	1	0.000	0.595
DNA damage signaling	1	0.001	0.037	80	0.223	1	5	0.043	0.822	40	0.061	0.693
Radiation sensitivity	1	0.001	0.037	6	0.002	0.088	18	0.077	0.822	11	0.014	0.621
Cell cycle regulator	1	0.001	0.037	116	0.330	1	4	0.042	0.822	20	0.030	0.571
Cell cycle pathway	1	0.001	0.037	237	0.729	0.949	17	0.075	0.822	55	0.104	0.593
Cell cycle	15	0.002	0.058	172	0.531	0.930	7	0.046	0.822	93	0.175	1
Cell cycle arrest	43	0.021	0.255	166	0.509	0.887	41	0.141	0.822	216	0.396	1
Ras pathway	39	0.016	0.209	7	0.002	0.284	64	0.186	0.822	312	0.565	1
MAPK cascade	50	0.040	0.418	16	0.021	0.494	57	0.177	0.822	107	0.204	1
# of sig. gene sets	62			32			10			39

Each method identified pathways related to p53 signaling and cell-cycle regulation. The ranks for these pathways were generally lower for GSOA than for the competing methods