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Table 3 Evaluation of over-representation analysis (ORA) outputs of bioinformatic tools employing KEGG pathways. Real (from dataset ST000284) and enriched data were used. The number of total metabolites in the pathway, the number of hits, the ranking of the pathway among all the KEGG pathways (according to their significance), the p-value and the adjusted p-value were calculated by the tools

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

Tool Data Rank Total metab. Hits P-value Adjusted p-value
Alanine, aspartate and glutamate metabolism
 ConsensusPathDB Real 2 28 8 3.77E-11 9.99E-10
Enriched 2 28 7 3.76E-13 7.32E-12
 IMPaLA Real 2 28 8 3.77E-11 7.91E-09
Enriched 2 28 7 3.76E-13 3.00E-10
 KEGGREST Real NA 28 7 NA NA
Enriched NA 28 7 NA NA
 MBRole (full database) Real 2 24 8 3.47E-12 2.07E-10
Enriched 1 24 7 7.23E-14 5.86E-12
 MBRole (Homo sapiens) Real 1 24 8 2.31E-11 1.50E-09
Enriched 1 24 7 3.85E-13 2.00E-11
 MetaboAnalyst (Fisher) Real 1 24 7 3.91E-06 6.74E-05
Enriched 1 24 7 6.21E-12 4.97E-10
 MetaboAnalyst (hyper.) Real 1 24 7 3.91E-06 6.74E-05
Enriched 1 24 7 6.21E-12 4.97E-10
 Metabox Real 2 32 8 3.60E-11 5.22E-10
Enriched 2 32 7 1.34E-13 1.27E-12
 MetExplore Real 3 NA 8 1.03E-08 4.32E-07
Enriched 2 NA 7 4.42E-10 1.33E-08
 MPEA (top down analysis) Real 1 24 8 4.41E-11 0.660
Enriched 1 24 7 5.01E-13 0.440
 MPEA (bottom up analysis) Real 1 24 8 1.01E-11 0.170
Enriched 1 24 7 1.08E-12 1.00
Aminoacyl-tRNA biosynthesis
 ConsensusPathDB Real 4 52 8 7.89E-10 1.05E-07
Enriched 9 52 5 2.58E-07 1.12E-06
 IMPaLA Real 4 52 8 7.89E-09 8.74E-07
Enriched 9 52 5 2.58E-07 1.13E-05
 KEGGREST Real NA 52 8 NA NA
Enriched NA 52 5 NA NA
 MBRole (full database) Real 5 75 8 6.07E-08 1.20E-06
Enriched 12 75 5 1.23E-06 8.30E-06
 MBRole (Homo sapiens) Real 5 75 8 3.75E-07 4.87E-06
Enriched 6 75 5 3.95E-06 3.42E-05
 MetaboAnalyst (Fisher) Real 3 75 8 1.40E-05 3.75E-04
Enriched 7 75 5 2.72E-05 3.11E-04
 MetaboAnalyst (hyper.) Real 3 75 8 1.40E-05 3.75E-04
Enriched 7 75 5 2.72E-05 3.11E-04
 Metabox Real 4 56 8 4.28E-09 3.10E-08
Enriched 4 56 5 8.69E-08 2.15E-07
 MetExplore Real 5 NA 8 1.55E-06 1.69E-06
Enriched 7 NA 5 1.51E-05 4.52E-04
 MPEA (top down analysis) Real 3 53 8 5.32E-09 1.00
Enriched 7 53 5 1.42E-06 1.00
 MPEA (Bottom up analysis) Real 5 53 8 7.12E-08 1.00
Enriched 4 53 5 6.57E-08 1.00
Arginine and proline metabolism
 ConsensusPathDB Real 9 76 7 2.79E-06 1.64E-05
Enriched 4 76 6 3.94E-08 3.85E-07
 IMPaLA Real 9 76 7 2.79E-09 8.74E-07
Enriched 4 76 6 3.94E-08 2.18E-06
 KEGGREST Real NA 77 7 NA NA
Enriched NA 77 6 NA NA
 MBRole (full database) Real 3 82 10 2.59E-10 8.55E-09
Enriched 2 82 8 9.30E-12 3.77E-10
 MBRole (Homo sapiens) Real 2 82 10 2.58E-09 8.38E-08
Enriched 2 82 8 6.21E-11 1.61E-09
 MetaboAnalyst (Fisher) Real 2 77 9 6.69E-06 6.74E-05
Enriched 2 77 8 8.61E-10 3.45E-08
 MetaboAnalyst (hyper.) Real 2 77 9 6.69E-06 6.74E-05
Enriched 2 77 8 8.61E-10 3.45E-08
 Metabox Real 9 84 7 1.92E-05 6.18E-05
Enriched 4 84 6 1.25E-08 5.96E-08
 MetExplore Real 2 NA 10 4.03E-08 1.69E-06
Enriched 1 NA 8 3.34E-10 1.00E-08
 MPEA (top down analysis) Real 4 90 10 1.40E-08 1.00
Enriched 2 90 7 1.09E-10 1.00
 MPEA (bottom up analysis) Real 2 90 10 2.24E-09 1.00
Enriched 2 90 8 1.69E-10 1.00
  1. NA means that information was not provided by the tool. Abbreviations: Fisher Fisher’s exact test, hyper hypergeometric test, NA not available
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