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Table 4 Evaluation of over-representation analysis (ORA) outputs of bioinformatic tools employing Reactome and HumanCyc 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 Reactome or HumanCyc 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
Reactome
 Metabolism of amino acids and derivates
  ConsensusPathDB Real 3 272 18 8.46E-14 4.55E-12
Enriched 1 272 12 7.67E-15 5.75E-13
  IMPaLA Real 3 272 18 8.46E-14 4.21E-11
Enriched 1 272 12 7.67E-15 1.02E-11
  PathVisio Real NA NA NA NA NA
Enriched NA NA NA NA NA
  Reactome Real 9 283 18 1.03E-04 3.81E-03
Enriched 1 283 12 8.18E-08 1.00E-05
HumanCyc
 tRNA charging
  ConsensusPathDB Real 2 24 8 9.14E-12 1.92E-10
Enriched 2 24 5 4.40E-09 1.30E-07
  HumanCyc Real 8 24 8 2.57E-05 0.002
Enriched 18 24 5 7.90E-05 4.25E-03
  IMPaLA Real 2 24 8 9.14E-12 2.28E-09
Enriched 2 24 5 4.40E-09 3.51E-07
  MBRole (full database) Real 4 64 8 8.38E-09 1.14E-06
Enriched 47 64 4 3.58E-07 7.97E-06
  MBRole (Homo sapiens) Real 5 64 8 1.26E-04 2.44E-03
Enriched 11 64 5 1.58E-04 1.52E-03
  MetExplore Real 1 NA 8 7.11E-07 7.75E-05
Enriched 6 NA 5 4.45E-05 3.60E-04
  1. NA means that information was not provided by the tool. Abbreviations: NA not available