Table 2 |
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|
Summary of locally distinct subgraphs of the yeast FOCI coexpression network |
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| Subgraph |
Number of genes |
Number unkown |
Major GO terms |
p-value |
|
|
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| A |
33 |
0 |
Protein biosynthesis (32) |
1.82e-30 |
| B |
67 |
2 |
Protein biosynthesis (64) |
2.20e-61 |
| C |
124 |
26 |
Ribosome biogenesis and assembly (74) |
2.10e-89 |
| D |
10 |
0 |
Glycolysis/gluconeogenesis (8) |
6.29e-20 |
| E |
7 |
1 |
Carboxylic/organic acid metabolism (4) |
5.07e-05 |
| F |
41 |
7 |
Ubiquitin dependent protein catabolism (21) |
1.37e-31 |
| G |
14 |
4 |
Cell organization and biogenesis (7) |
1.60e-04 |
| H |
7 |
0 |
Main pathways of carbohydrate metabolism (4) |
2.46e-07 |
| I |
13 |
0 |
Electron transport (7) |
2.00e-15 |
| J |
13 |
0 |
Glutamate biosynthesis/TCA cycle (4) |
7.09e-10 |
| K |
71 |
25 |
Response to stress (17); carbohydrate metabolism (13) |
3.94e-11 |
| L |
10 |
4 |
Response to stress (2) |
3.35e-02 |
| N |
149 |
51 |
Sporulation (27) |
2.23e-29 |
| M |
5 |
2 |
Mitochondrial matrix (5); mitochondrial ribosome (4) |
2.83e-09 |
| O |
7 |
2 |
Meiosis (4) |
3.77e-07 |
| P |
52 |
13 |
Cell proliferation (32); DNA replication and chromosome cycle (28) |
1.12e-28 |
| Q |
26 |
21 |
Telomerase-independent telomere maintenance (5) |
1.82e-14 |
| R |
7 |
0 |
Chromatin assembly/disassembly (7) |
4.25e-18 |
| S |
14 |
5 |
Cell wall (4); bud (4) |
4.47e-05 |
| T |
24 |
8 |
Cell proliferation (15); mitotic cell cycle (9) |
6.54e-16 |
| U |
21 |
4 |
Cell separation during cytokinesis (4); cell proliferation (9); cell wall organization
and biogenesis (5) |
5.27e-10 |
| V |
12 |
4 |
Metabolism (7) |
2.48e-02 |
| W |
10 |
9 |
Nine of ten are members of the seripauperin gene family |
NA |
| X |
9 |
0 |
Sulfur amino acid metabolism (6); amino acid metabolism (3) |
3.33e-13 |
| Y |
7 |
1 |
Cell growth and maintenance (6) |
7.50e-04 |
| Z |
19 |
2 |
Conjugation with cellular fusion (13) |
1.82e-21 |
| AA |
8 |
4 |
Biotin biosynthesis (2) |
1.81e-06 |
| BB |
7 |
0 |
Response to abiotic stimulus (2) |
1.48e-02 |
| CC |
9 |
5 |
Six of nine members belong to COS family of subtelomerically encoded proteins |
NA |
| DD |
18 |
7 |
Cell growth and/or maintenance (8) |
4.43e-03 |
| EE |
11 |
3 |
Vitamin B6 metabolism (2) |
2.58e-05 |
| FF |
7 |
0 |
Ty element transposition (7) |
6.01e-14 |
|
|
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|
The columns of the table summarize the total size of the locally distinct subgraph, the number of genes in the subgraph that are unannotated (according to the GO Slim annotation from the Saccharomyces Genome Database of December 2003), the primary GO term(s) associated with the subgraph, and a p-value indicating the frequency at which one would expect to find the same number of genes assigned to the given GO term in a random assemblage of the same size. |
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|
Magwene and Kim Genome Biology 2004 5:R100 doi:10.1186/gb-2004-5-12-r100 |
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