Table 2

Statistics of functional enrichment

Phylogeny Method

Counting Method


Organism

Fraction

P-value

Fraction

P-value

P-value ratioa


Aeropyrum pernix

39/45

6.33E-12

40/46

2.21E-12

0.349

Aquifex aeolicus

80/107

1.23E-32

81/111

8.71E-32

7.08

Bacillus subtilis

329/503

1.86E-44

363/601

4.10E-38

2.20E+06

Buchnera sp.

167/246

1.28E-31

181/307

1.90E-23

1.48E+08

Chlamydia trachomatis

95/132

3.94E-24

123/295

1.88E-03

4.77E+20

Chlamydophia pneumoniae

104/137

5.03E-30

135/327

4.29E-03

8.53E+26

Deinococcus radiodurans

173/221

4.07E-57

167/218

5.56E-52

1.37E+05

Escherichia coli K12

439/750

8.92E-48

606/1553

0.19

2.13E+46

Halobacterium sp.

127/150

7.60E-38

125/145

6.27E-39

0.0825

Helicobacter pylori 26695

120/151

1.11E-37

122/158

4.92E-36

0.443

Lactococcus lactis

182/277

2.79E-28

196/319

4.19E-25

1500

Methanococcus janaschii

68/83

5.82E-22

64/79

5.91E-20

102

Mycobacterium tuberculosis

203/293

1.05E-42

226/347

1.09E-41

10.4

Mycoplasma pulmonis

75/98

3.61E-11

77/103

1.44E-10

3.99

Neisseria meningitidis MC58

150/222

1.25E-51

156/241

9.14E-51

7.31


a Ratio is P-value for functional enrichment by the phylogeny method divided by P-value for functional enrichment by the counting method [i.e., (column 3) / (column 5)].

Zheng et al. BMC Bioinformatics 2005 6:243   doi:10.1186/1471-2105-6-243

Open Data