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Table 1 Summary of queries for 38 metabolic pathways against the yeast FOCI coexpression network

From: Estimating genomic coexpression networks using first-order conditional independence

Pathway

Number of genes(in KEGG)

Size of largest coherent subnetwork(s)

Carbohydrate metabolism

  

Glycolysis/gluconeogenesis

41 (47)

18*

Citrate cycle (TCA cycle)

27 (30)

18*

Pentose phosphate pathway

20 (27)

6*

Fructose and mannose metabolism

39 (46)

4

Galactose metabolism

25 (30)

8*

Ascorbate and aldarate metabolism

11 (13)

3

Pyruvate metabolism

32 (34)

8*

Glyoxylate and dicarboxylate metabolism

12 (14)

6*

Butanoate metabolism

27 (30)

7*

Energy metabolism

  

Oxidative phosphorylation

53 (76)

31*

ATP synthesis

21 (30)

7*

Nitrogen metabolism

24 (27)

3

Lipid metabolism

  

Fatty acid metabolism

13 (17)

3

Nucleotide metabolism

  

Purine metabolism

87 (99)

34*

Pyrimidine metabolism

72 (80)

15*

Nucleotide sugars metabolism

11 (14)

2

Amino acid metabolism

  

Glutamate metabolism

25 (27)

3

Alanine and aspartate metabolism

26 (27)

7*

Glycine, serine and threonine metabolism

36 (42)

7*

Methionine metabolism

13 (14)

6*

Valine, leucine and isoleucine biosynthesis

15 (16)

10*

Lysine biosynthesis

16 (20)

3

Lysine degradation

26 (30)

4

Arginine and proline metabolism

20 (24)

5*

Histidine metabolism

20 (25)

3

Tyrosine metabolism

27 (34)

2

Tryptophan metabolism

20 (25)

2

Phenylalanine, tyrosine and tryptophan biosynthesis

21 (23)

6*

Metabolism of complex carbohydrates

  

Starch and sucrose metabolism

118 (139)

29

N-Glycans biosynthesis

43 (49)

13*

O-Glycans biosynthesis

18 (20)

2

Aminosugars metabolism

16 (20)

2

Keratan sulfate biosynthesis

18 (20)

2

Metabolism of complex lipids

  

Glycerolipid metabolism

56 (68)

12*

Inositol phosphate metabolism

87 (103)

10

Sphingophospholipid biosynthesis

101 (118)

11

Metabolism of cofactors and vitamins

  

Vitamin B6 metabolism

11 (14)

2

Folate biosynthesis

14 (17)

1

  1. The values in the second column represent the number of pathway genes represented in the GCC of the yeast FOCI graph, with the total number of genes assigned to the given pathway in parentheses. The third column indicates the number of pathway genes in the largest coherent subgraph resulting from each pathway query. Pathways represented by coherent subgraphs that are significantly larger than are expected at random (p < 0.05) are marked with asterisks.
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Genome Biology

ISSN: 1474-760X

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