Table 2.

Summary of the tools used to assess the performance of over-representation (ORA) methods and their main characteristics (July 2017). Tools and databases are sorted alphabetically

Tool name	Tool version	Database used	Database version	Test used in this work	Platform	Input code	Website
ConsensusPathDB	32	HumanCyc KEGG Reactome	19.1 (06/2015) 80.0 (10/2016) 59 (12/2016)	Fisher’s exact test Fisher’s exact test Fisher’s exact test	Online	HumanCyc KEGG Reactome	http://cpdb.molgen.mpg.de/
HumanCyc	21.0	HumanCyc	21.0 (12/2016)	Fisher’s exact test	Online	Name	https://humancyc.org/
IMPaLA	10	HumanCyc KEGG Reactome	NA NA NA	Fisher’s exact test Fisher’s exact test Fisher’s exact test	Online	HumanCyc KEGG Reactome	http://impala.molgen.mpg.de/
IPA®	NA	IPA® disease	NA	Fisher’s exact test, Z-score	Java-based software	KEGG
KEGGREST	1.17.0	KEGG	NA	–	R	KEGG	https://bioconductor.org/packages/release/bioc/html/KEGGREST.html
MBRole	2.0	HMDB disease HumanCyc KEGG	3.5 (01/2013) 17.1 (06/2013) 54.1 (05/2010)	Hypergeometric test Hypergeometric test Hypergeometric test	Online	HumanCyc KEGG	http://csbg.cnb.csic.es/mbrole2/
MetaboAnalyst	3.0	SMPDB disease KEGG	NA NA	Fisher’s exact test, hypergeometric test Fisher’s exact test, hypergeometric test	Online	KEGG	http://www.metaboanalyst.ca/
Metabox	NA	KEGG	NA	Hypergeometric test	R	PubChem	https://github.com/kwanjeeraw/metabox
MetaCore™	NA	MeSH and OMIM disease	NA	–	Online	PubChem	https://portal.genego.com/
MetExplore	2.11.2	HumanCyc KEGG	18.0 (02/2014) 74.0 (04/2015)	Fisher’s exact test Fisher’s exact test	Online	HumanCyc KEGG	http://metexplore.toulouse.inra.fr/metexplore2/
MPEA	(2010)	KEGG	(2010)	Hypergeometric test	Online	KEGG	http://ekhidna.biocenter.helsinki.fi/poxo/mpea
PathVisio	3.2.4	Reactome	54 (10/2015)	Z-score	Java-based software	KEGG	https://www.pathvisio.org/
Reactome	61	Reactome	61 (06/2017)	Fisher’s exact test	Online	KEGG	http://reactome.org/

Abbreviations: NA not available