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Table 12 KEGG pathway classes that are significantly enriched or depleted for reactions with links to MetaCyc

From: A systematic comparison of the MetaCyc and KEGG pathway databases

Status Pathway class Class size Links p-value
Enriched Nucleotide And Amino Acid Metabolism 72 346 419 2.6 × 10−56
Enriched Carbohydrate Metabolism 15 496 766 4.1 × 10−29
Enriched Amino Acid Metabolism 13 478 784 3.0 × 10−20
Enriched Energy Metabolism 8 167 246 2.9 × 10−14
Enriched Cofactor And Vitamin Biosynthesis 19 104 133 1.8 × 10−11
Enriched Energy Metabolism 24 89 114 1.3 × 10−10
Enriched Carbon Fixation 13 56 66 7.6 × 10−8
Enriched Aromatic Amino Acid Metabolism 11 45 55 2.2 × 10−5
Enriched Alkaloid And Other Secondary Metabolite Biosynthesis 4 28 30 2.9 × 10−5
Enriched Other Carbohydrate Metabolism 6 37 44 2.9 × 10−5
Enriched Nucleotide Metabolism 2 159 261 7.6 × 10−5
Enriched Cysteine And Methionine Metabolism 6 27 30 3.4 × 10−4
Enriched Central Carbohydrate Metabolism 13 42 52 4.4 × 10−4
Enriched Reaction Motif 3 15 15 7.1 × 10−3
Enriched Arginine And Proline Metabolism 3 15 15 7.1 × 10−3
Enriched Histidine Metabolism 2 14 14 1.6 × 10−2
Enriched Purine Metabolism 3 23 28 2.1 × 10−2
Depleted Xenobiotics Biodegradation And Metabolism 20 258 1013 1.0 × 10−37
Depleted Glycan Biosynthesis And Metabolism 15 36 254 1.9 × 10−21
Depleted Metabolism Of Terpenoids And Polyketides 20 265 848 4.4 × 10−13
Depleted Glycan Metabolism 10 0 51 6.8 × 10−11
Depleted Glycosaminoglycan Metabolism 7 0 30 2.0 × 10−5
Depleted Lipid Metabolism 17 245 713 1.4 × 10−3
  1. Class size is the number of pathway instances for the given pathway class. The ‘Links’ column is the number of reactions among the pathways of the pathway class that have links to MetaCyc reactions, over the total number of reactions for the pathway class. The Bonferroni-corrected p-value from the hypergeometric test indicates the probability that the observed proportion of reactions with links within the pathway occurred by chance. Pathways with a p-value at or below a cut-off of α = 0.025 are shown. The full list may be found in the Additional file 2.
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BMC Bioinformatics

ISSN: 1471-2105

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