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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.