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