Table 1.

Publicly available software tools and web-applications for analyzing cellular pathway activity changes in omics datasets; some of the methods can be applied directly in the web browser (see column 4), and some of the tools provide advanced visualization features to facilitate the interpretation of the results (see column 5)

Method type	Software name	Availability	Web application	Visualization features	Reference
Over-representation analysis (ORA) tools	DAVID	https://david.ncifcrf.gov	Yes	No	Dennis et al. 2003
	GOstat	http://gostat.wehi.edu.au	Yes	Yes	Beißbarth and Speed 2004
	OntoExpress	http://vortex.cs.wayne.edu/ontoexpress	Yes	No	Draghici et al. 2003
	GoMiner	https://discover.nci.nih.gov/gominer	Yes	Yes	Zeeberg et al. 2003
	GOToolBox	http://genome.crg.es/GOToolBox	Yes	No	Martin et al. 2004
Geneset enrichment analysis (GSEA) tools	GSEA	http://software.broadinstitute.org/gsea	No	Yes	Subramanian et al. 2005
	GAGE	http://bioconductor.org/packages/release/bioc/html/gage.html	No	No	Luo et al. 2009
	GSA	http://statweb.stanford.edu/~tibs/GSA	No	No	Efron and Tibshirani 2007
	PAGE / PGSEA	https://www.bioconductor.org/packages/release/bioc/html/PGSEA.html	No	No	Kim and Volsky 2005
	GLOBALTEST	https://bioconductor.org/packages/release/bioc/html/globaltest.html	No	Yes	Goeman et al. 2004
	PADOG	http://bioconductor.org/packages/release/bioc/html/PADOG.html	No	No	Tarca et al. 2012
Network module-based pathway analysis (NMPA)	FunMOD	https://sourceforge.net/projects/funmodnetwork	No	Yes	Natale et al. 2014
	PINA	http://cbg.garvan.unsw.edu.au/pina	Yes	Yes	Cowley et al. 2012
	ReactomeFIViz	http://wiki.reactome.org/index.php/ReactomeFIViz	No	Yes	Wu et al. 2014
Network topology-based pathway analysis (NMPA)	PWEA	https://zlab.bu.edu/PWEA	No	Yes	Hung et al. 2010
	SPIA	http://bioconductor.org/packages/release/bioc/html/SPIA.html	No	Yes	Tarca et al. 2009
	PathNet	http://bioconductor.org/packages/release/bioc/html/PathNet.html	No	No	Dutta et al. 2012
	DeGraph	https://bioconductor.org/packages/release/bioc/html/DEGraph.html	No	Yes	Jacob et al. 2012
	EnrichNet	http://www.enrichnet.org	Yes	Yes	Glaab et al. 2012
	Ontologizer	http://ontologizer.de	Yes	Yes	Bauer et al. 2008
	SANTA	http://bioconductor.org/packages/release/bioc/html/SANTA.html	No	Yes	Cornish and Markowetz 2014
	ToPASeq	https://bioconductor.org/packages/release/bioc/html/ToPASeq.html	No	Yes	Ihnatova and Budinska 2015