Table 1 |
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|
Summary of queries for 38 metabolic pathways against the yeast FOCI coexpression network |
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| 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 |
|
|
||
|
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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|
Magwene and Kim Genome Biology 2004 5:R100 doi:10.1186/gb-2004-5-12-r100 |
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