Table 3 (detailed)
Table 3 is
reproduced here listing all enriched functional categories among the 6 clusters
of Figure 2. p-values
are calculated using the hypergeometric test
(equivalently the one-sided Fisher 2x2 statistic) as follows:
Here, # in
FC in cluster corresponds to a, # in
FC over all clusters corresponds to f,
# of genes in cluster corresponds to c,
and n = 175 (since this many genes
are clustered in total).
cluster |
p-value |
function-designation |
description |
# in FC in cluster |
# in FC over all
clusters |
# of genes in cluster |
0 |
7.06E-05 |
5.5 |
adaptation to stress |
12 |
14 |
61 |
0 |
5.38E-04 |
5.5.1 |
osmotic pressure |
10 |
12 |
61 |
1 |
8.99E-05 |
1.7.34 |
peptidoglycan (murein) turnover,
recycling |
3 |
4 |
6 |
1 |
1.93E-04 |
6 |
cell structure |
6 |
44 |
6 |
1 |
2.22E-04 |
6.2 |
peptidoglycan (murein) |
3 |
5 |
6 |
1 |
8.12E-04 |
4.S |
substrate |
5 |
32 |
6 |
1 |
1.96E-03 |
4 |
transport |
5 |
38 |
6 |
1 |
5.70E-03 |
4.3.A |
Pyrophosphate Bond (ATP;
GTP; P2) Hydrolysis-driven Active Transporters |
3 |
13 |
6 |
1 |
5.70E-03 |
4.3.A.1 |
The ATP-binding Cassette
(ABC) Superfamily + ABC-type Uptake Permeases |
3 |
13 |
6 |
1 |
5.70E-03 |
4.3 |
Primary Active
Transporters |
3 |
13 |
6 |
1 |
5.73E-03 |
4.3.A.1.a |
ABC superfamily
ATP binding cytoplasmic component |
2 |
4 |
6 |
2 |
4.32E-03 |
1.6 |
macromolecules (cellular
constituent) biosynthesis |
6 |
9 |
39 |
2 |
5.03E-03 |
1.1.1 |
carbon compounds |
11 |
24 |
39 |
2 |
9.11E-03 |
6.4 |
flagellum |
4 |
5 |
39 |
2 |
9.11E-03 |
1.6.12 |
flagella |
4 |
5 |
39 |
2 |
9.11E-03 |
5.3 |
motility (incl. chemotaxis, energytaxis, aerotaxis, redoxtaxis) |
4 |
5 |
39 |
2 |
9.23E-03 |
1.1 |
carbon utilization |
12 |
29 |
39 |
3 |
9.29E-04 |
1.7.1 |
unassigned reversible
reactions |
3 |
3 |
18 |
4 |
8.13E-06 |
1.5 |
building block
biosynthesis |
13 |
27 |
27 |
4 |
4.41E-04 |
1.5.1 |
amino acids |
9 |
19 |
27 |
5 |
7.06E-04 |
4.S |
substrate |
11 |
32 |
24 |
5 |
8.77E-04 |
4 |
transport |
12 |
38 |
24 |
5 |
2.31E-03 |
4.4.A.6 |
The PTS Mannose-Fructose-Sorbose (Man) Family |
3 |
3 |
24 |
5 |
6.45E-03 |
1.1 |
carbon utilization |
9 |
29 |
24 |
5 |
6.70E-03 |
1.1.1 |
carbon compounds |
8 |
24 |
24 |
5 |
7.34E-03 |
4.4 |
Group Translocators |
4 |
7 |
24 |
5 |
7.34E-03 |
4.4.A |
Phosphotransferase Systems (PEP-dependent PTS) |
4 |
7 |
24 |