GAGE: generally applicable gene set enrichment for pathway analysis

BMC Bioinformatics

Table 4 Comparison between GAGE, PAGE and GSEA-g results from the BMP6-MSC dataset

Gene Sets & Methods		Top 10 abs(T/Z)	Top 10 p-values	Sign. Sets
Experiment Sets	GAGE	2.48	7.3E-04	39 (13)
	PAGE	24.6	1.3E-131	864 (940)
	GSEA-g	1.97	<1.0E-3	86 (77)
Canonical Pathways	GAGE	1.61	2.0E-2	7 (2)
	PAGE	10.9	8.8E-28	248 (297)
	GSEA-g	1.53	6.8E-2	6 (0)

The significantly enriched experimental sets and canonical pathways in human MSC following 8 hour BMP6 treatment were inferred by GAGE, PAGE and GSEA-g (permutation of gene labels). Top 10 t- (GAGE) or z- (PAGE) statistics or NES (GSEA) and p-values and the numbers of significant gene sets were shown with p-value ≤ 0.01 (or FDR q-value ≤ 0.10). Note that GSEA-g results shown were based on nominal p-values (or FDR q-values).

ISSN: 1471-2105