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Table 4 Enrichment test for an informative data source in the GO hierarchy

From: Integrative approaches to the prediction of protein functions based on the feature selection

Data source

GO term

Description

P-value

NO

NOPW

OPHID (PPI)

0001775

cell activation

1.24E-08

69

24

 

0046649

lymphocyte activation

1.47E-07

57

20

 

0016070

RNA metabolic process

1.90E-07

44

17

 

0045321

leukocyte activation

3.03E-07

64

21

 

0046651

lymphocyte proliferation

8.95E-07

16

9

Interpro (Domain)

0006811

ion transport

2.68E-07

23

18

 

0006812

cation transport

5.32E-07

15

13

 

0006807

nitrogen compound metabolic process

7.76E-07

57

34

Pfam (Domain)

0044271

nitrogen compound biosynthetic process

0

10

10

 

0006807

nitrogen compound metabolic process

3.98E-11

57

43

 

0009308

amine metabolic process

2.47E-09

52

38

 

0006519

amino acid and derivative metabolic process

5.53E-09

51

37

 

0006725

aromatic compound metabolic process

4.85E-08

25

21

 

0006520

amino acid metabolic process

5.36E-08

30

24

 

0006091

generation of precursor metabolites and energy

1.25E-07

15

14

 

0006811

ion transport

3.21E-07

23

19

MGI (Phenotype)

0001775

cell activation

3.42E-08

69

25

 

0046649

lymphocyte activation

2.61E-07

57

21

 

0045321

leukocyte activation

6.25E-07

64

22

BioMart (Phylogenetic profile)

0046164

alcohol catabolic process

1.21E-08

6

4

 

0030100

regulation of endocytosis

5.89E-07

5

3

 

0046365

monosaccharide catabolic process

5.89E-07

5

3

Inparanoid (Phylogenetic profile)

0001775

cell activation

3.45E-11

69

17

 

0051239

regulation of multicellular organismal process

3.58E-11

88

19

 

0050865

regulation of cell activation

2.70E-09

42

12

 

0046649

lymphocyte activation

1.76E-08

57

13

 

0045321

leukocyte activation

8.80E-08

64

13

 

0019220

regulation of phosphate metabolic process

1.93E-07

13

6

 

0051174

regulation of phosphorus metabolic process

3.74E-07

14

6

 

0042325

regulation of phosphorylation

6.77E-07

10

5

 

0051249

regulation of lymphocyte activation

9.39E-07

37

9

OMIM (Diseases)

0006812

cation transport

1.62E-05

15

4

 

0006118

electron transport

5.17E-05

4

2

Zhang et al (Gene expression)

0040013

negative regulation of locomotion

3.21E-06

3

2

 

0000279

M phase

5.70E-06

19

4

 

0019882

antigen processing and presentation

3.14E-05

5

2

 

0008380

RNA splicing

6.22E-05

6

2

 

0007049

cell cycle

8.95E-05

52

5

Su et al (Gene expression)

0050953

sensory perception of light stimulus

5.59E-06

4

2

 

0019882

antigen processing and presentation

1.39E-05

5

2

 

0007059

chromosome segregation

1.39E-05

5

2

SAGE (Gene expression)

0019882

antigen processing and presentation

4.45E-06

5

2

 

0050851

antigen receptor-mediated signaling pathway

1.54E-05

7

2

 

0042110

T cell activation

3.93E-05

26

3

 

0030217

T cell differentiation

5.21E-05

10

2

 

0019395

fatty acid oxidation

6.34E-05

2

1

  1. The data source in the first column is informative for predicting gene functions belonging to the GO terms in the second column and its off-spring GO terms. The p-values in the fourth column represent the significance of the number of off-springs that are well predicted using the given data source. This table presents GO terms having p-value <1.00E-04 and having a sufficient number of off-springs. The bold and italic fonts indicate the significant GO terms based on the enrichment tests from the exhaustive search feature selection and the KL1LR method for the given data source. Among them, if the data source is informative for the GO term itself, the GO term is underlined (see the main text for more explanation). NO stands for the number of all off-springs of a GO term and NOPW for the number of off-springs predicted well using a given data source.
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BMC Bioinformatics

ISSN: 1471-2105

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