GAGE: generally applicable gene set enrichment for pathway analysis

BMC Bioinformatics

Table 2 Comparison between GAGE, PAGE and GSEA results from the two lung cancer datasets

Gene Sets & Methods		Overlap	Top 10 p-values	Metastasis	Tumor	Sign. Sets
Experimental Sets	GAGE	4	4.2E-35, 2.4E-13	3, 5	6, 7	242 (283), 120 (124)
	PAGE	4	1.0E-170, 2.0E-85	6, 4	8, 6	698 (757), 585 (655)
	GSEA	1	5.7E-3, 6.4E-3	1, 2	6, 4	3 (0), 4 (0)
Canonical Pathways	GAGE	5	6.7E-6, 7.5E-4	10, 9	10, 9	20 (16), 10 (8)
	PAGE	4	4.2E-26, 3.7E-27	2, 3	4, 3	170 (202), 153 (186)
	GSEA	0	1.1E-2, 1.4E-2	1, 1	5, 5	2 (0), 4 (0)

The top 10 most significantly enriched experimental sets and canonical pathways in poor clinical outcomes vs good outcomes were inferred by GAGE, PAGE, and GSEA from two published lung adenocarcinoma data sets used in the GSEA paper [3]. Data columns are overlap between top 10 gene sets for the two studies, top 10 p-values, number of top 10 gene sets related to metastasis (bt) and tumor (t and bt), and numbers of significant gene sets with p-value ≤ 0.001 (or FDR q-value ≤ 0. 01).

ISSN: 1471-2105