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 | |
HumanCyc | 21.0 | HumanCyc | 21.0 (12/2016) | Fisher’s exact test | Online | Name | |
IMPaLA | 10 | HumanCyc KEGG Reactome | NA NA NA | Fisher’s exact test Fisher’s exact test Fisher’s exact test | Online | HumanCyc KEGG Reactome | |
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 | |
MetaboAnalyst | 3.0 | SMPDB disease KEGG | NA NA | Fisher’s exact test, hypergeometric test Fisher’s exact test, hypergeometric test | Online | KEGG | |
Metabox | NA | KEGG | NA | Hypergeometric test | R | PubChem | |
MetaCore™ | NA | MeSH and OMIM disease | NA | – | Online | PubChem | |
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 | |
MPEA | (2010) | KEGG | (2010) | Hypergeometric test | Online | KEGG | |
PathVisio | 3.2.4 | Reactome | 54 (10/2015) | Z-score | Java-based software | KEGG | |
Reactome | 61 | Reactome | 61 (06/2017) | Fisher’s exact test | Online | KEGG |