Table 2 Summary of locally distinct subgraphs of the yeast FOCI coexpression network
From: Estimating genomic coexpression networks using first-order conditional independence
Subgraph | Number of genes | Number unkown | Major GO terms | p-value |
|---|---|---|---|---|
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 |