Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

BMC Proceedings

Table 2 Summary of the analytical approaches and choice of software for each group

Group	Analytical tool	Class^a	Key statistical method
University of Cordoba, Spain [25]	ArrayUnlock [31]	MEA	Hypergeometric; Chi Square-test
	Ingenuity Pathway Analysis [32]	SEA	Fisher's exact test
Institute for Animal Health, Compton, UK [27]	MAPPFinder/GenMAPP [14, 33, 34]	SEA	Z-score; Hypergeometric
Aarhus University, Denmark [24]	LIMMA [35]	SEA	Wilcoxon
	TopGO [30]	MEA	Fisher's exact test; Kolmogorov Smirnoff
	Globaltest [36]	GSEA	Global test
	GIST [37]	-	support vector machine classification; kernel principal components analysis
Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands [23]	AnnotationDbi [38]	-	-
	GOstats [39]	SEA	Hypergeometric
Animal Breeding and Genomics Centre, Animal Sciences Group, Lelystad, The Netherlands [28]	Globaltest [36]	GSEA	Global test
	GOEAST [40]	SEA	Fisher's exact; Hypergeometric; Chi Square-test
INRA, Toulouse and Rennes [26]	GOTM [41]	SEA, GSEA	Hypergeometric
	Pathway Studio [42]	-	Subnetwork Enrichment Analysis (SNEA), one-sided Mann-Whitney U-Test
	Ingenuity Pathway Analysis [32]	SEA	Fisher's exact test

^a SEA, singular enrichment analysis; GSEA, gene set enrichment analysis; MEA, modular enrichment analysis, as suggested by Huang et al [15]

ISSN: 1753-6561