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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

From: Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data

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/
  1. Abbreviations: NA not available