Table 1.

Examples of software available for gene set analysis, divided into three major families of algorithms: over-representation, enrichment, and differential variability analyses.

ANALYSIS FAMILY	METHODS	AVAILABILITY	REFERENCE
Over-representation	GeneMAPP	http://www.genmapp.org/	19,20
	GoMiner	http://discover.nci.nih.gov/gominer/	21
	GatiGo	http://bioinfo.cipf.es/babelomicswiki/tool:fatigo	22
	Gostat	http://gostat.wehi.edu.au/	23
	FunAssociate	http://llama.mshri.on.ca/funcassociate/	24
	GOToolBox	http://genome.crg.es/GOToolBox/	25
	GeneMergeGOEAST	http://www.oeb.harvard.edu/faculty/hartl/old_site/lab/publications/Genemerge.html	26
	ClueGo	http://omicslab.genetics.ac.cn/GOEAST/	27
	FunSpec	http://www.ici.upmc.fr/cluego/	28
	Go:TermFinder	http://funspec.med.utoronto.ca/	29
	WebGestalt	http://go.princeton.edu/cgi-bin/GoTermFinder	30
	agriGo	http://bioinfo.vanderbilt.edu/webgestalt/	31
		http://bioinfo.cau.edu.cn/agriGo/	32
Enrichment	GSEA	http://www.broadinstitute.org/gsea	16
	SAFE	Bioconductor (safe)	33
	LIMMA	Bioconductor (LIMMA)	34
	DAVID	http://david.abcc.ncifcrf.gov/list.jsp	35
	TopGO	Bioconductor (topGo)	36
	Gage	Bioconductor (gage)	37
	sigPathway	Bioconductor (sigPathway)	38
Differential variability	DIRAC	Bioconductor (GS-Reg)	10
	EVA	Bioconductor (GS-Reg)	39
	GINEA	No implementation	40
	IB-GSA	No implementation	18
	MAVTgsa	CRAN	41
	synergy	http://www.biomedcentral.com/content/supplementary/1752-0509-2-10-s3.pdf	42