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 | |