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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.