Skip to main content

Table 11 MetaCyc pathway classes that are significantly enriched or depleted for reactions with links to KEGG

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

Status Pathway class Class size Links p-value
Enriched Amino Acids Biosynthesis 112 186 260 1.4 × 10−20
Enriched Individual Amino Acids Biosynthesis 99 174 244 4.0 × 10−19
Enriched Amino Acids Degradation 118 222 326 2.0 × 10−17
Enriched Purine Nucleotide Biosynthesis 19 46 56 3.2 × 10−10
Enriched Generation Of Precursor Metabolites And Energy 162 170 304 2.6 × 10−9
Enriched C1 Compounds Utilization And Assimilation 28 75 102 9.3 × 10−9
Enriched Autotrophic CO2 Fixation 7 47 57 1.3 × 10−7
Enriched CO2 Fixation 9 48 59 2.8 × 10−7
Enriched Vitamins Biosynthesis 68 128 223 1.4 × 10−6
Enriched Sugar Derivatives Degradation 42 109 162 3.8 × 10−6
Enriched Sugar Alcohols Degradation 12 54 68 6.0 × 10−6
Enriched Amines And Polyamines Biosynthesis 37 57 74 6.9 × 10−6
Enriched Carboxylates Degradation 44 82 132 1.0 × 10−5
Enriched Sugars Degradation 51 108 162 1.5 × 10−5
Enriched NAD Biosynthesis 8 23 23 1.6 × 10−5
Enriched Fermentation 46 75 106 3.6 × 10−5
Enriched Nucleosides And Nucleotides Biosynthesis 35 69 128 6.8 × 10−5
Enriched Nucleosides And Nucleotides Degradation 29 64 90 1.4 × 10−4
Enriched Purine Nucleotide Salvage 13 26 28 1.7 × 10−4
Enriched Arginine Degradation 15 35 42 4.6 × 10−4
Enriched Purine Nucleotide De Novo Biosynthesis 6 22 30 4.9 × 10−4
Enriched Mandelates Degradation 2 18 18 9.9 × 10−4
Enriched Gluconeogenesis 2 23 28 1.1 × 10−3
Enriched Glycolysis 6 27 30 2.0 × 10−3
Enriched NAD Metabolism 11 28 33 2.1 × 10−3
Enriched Geranylgeranyldiphosphate Biosynthesis 3 18 18 2.3 × 10−3
Enriched Catechol Degradation 7 17 17 2.3 × 10−3
Enriched Methionine Biosynthesis 13 29 34 4.0 × 10−3
Enriched Photosynthesis 5 24 30 4.0 × 10−3
Enriched Pyrimidine Nucleotide Biosynthesis 8 36 53 5.7 × 10−3
Enriched Toluenes Degradation 13 35 46 7.2 × 10−3
Enriched Glutamate Degradation 10 28 35 1.5 × 10−2
Enriched Formaldehyde Assimilation 3 24 28 1.6 × 10−2
Enriched Alcohols Degradation 17 24 30 1.6 × 10−2
Enriched Urate Degradation 2 17 18 2.4 × 10−2
Enriched Cobalamin Biosynthesis 9 35 46 2.5 × 10−2
Depleted Secondary Metabolites Biosynthesis 460 579 1896 3.8 × 10−35
Depleted Glucosinolates Biosynthesis 9 4 104 2.0 × 10−17
Depleted Biosynthesis 1182 1459 4215 2.3 × 10−16
Depleted Nitrogen Containing Glucosides Biosynthesis 13 11 125 8.0 × 10−15
Depleted Hormones Degradation 24 12 124 2.7 × 10−13
Depleted Polymeric Compounds Degradation 35 17 136 3.5 × 10−12
Depleted Polysaccharides Degradation 33 17 127 2.0 × 10−10
Depleted Steroids Degradation 8 2 46 4.2 × 10−6
Depleted Polyketides Biosynthesis 13 6 62 1.5 × 10−5
Depleted Glucosinolates Degradation 4 0 30 7.0 × 10−5
Depleted Cholesterol Degradation 4 1 33 3.3 × 10−4
Depleted Fatty Acid Biosynthesis 49 20 354 3.4 × 10−4
Depleted Nitrogen Containing Secondary Compounds Degradation 18 13 77 1.0 × 10−3
Depleted Terpenoids Biosynthesis 127 176 530 1.2 × 10−3
Depleted Plant Hormones Degradation 15 7 55 1.6 × 10−3
Depleted Sesquiterpenoids Biosynthesis 32 25 114 1.6 × 10−3
Depleted Chlorotoluene Degradation 5 0 24 2.3 × 10−3
Depleted Auxins Degradation 8 0 23 4.1 × 10−3
Depleted Apocarotenoids Biosynthesis 4 0 20 2.4 × 10−2
Depleted Lignans Biosynthesis 5 0 20 2.4 × 10−2
  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 KEGG 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.