Table 1

Differentially represented Gene Ontology categories

Category

Term

Count*

Percent

P value


Biological process

Lipid metabolism

110

6.10

3.10E-09

Steroid metabolism

41

2.30

9.90E-09

Cellular lipid metabolism

78

4.30

9.30E-08

Response to toxin

34

1.90

4.20E-06

Response to biotic stimulus

94

5.20

7.90E-06

Transport

309

17.10

9.20E-06

Defense response

92

5.10

9.60E-06

Response to chemical stimulus

66

3.60

9.80E-06

Response to abiotic stimulus

84

4.60

1.20E-05

Localization

352

19.40

1.40E-05

Metabolism

799

44.10

1.70E-05

DNA-dependent DNA replication

22

1.20

3.60E-05

Establishment of localization

340

18.80

3.70E-05

Physiological process

1,041

57.50

4.30E-05

DNA replication

36

2.00

1.60E-04

Cellular physiological process

958

52.90

2.50E-04

Secretion

48

2.70

2.80E-04

Electron transport

74

4.10

3.00E-04

Response to stress

66

3.60

3.20E-04

Response to stimulus

191

10.50

3.50E-04

Secretory pathway

45

2.50

4.30E-04

Response to endogenous stimulus

31

1.70

7.80E-04

Response to DNA damage stimulus

28

1.50

8.10E-04

Sleep

7

0.40

1.00E-03

Primary metabolism

705

38.90

1.50E-03

Protein complex assembly

28

1.50

2.60E-03

Intracellular transport

99

5.50

2.90E-03

DNA repair

25

1.40

2.90E-03

Intracellular protein transport

80

4.40

3.90E-03

Regulation of neurotransmitter levels

26

1.40

4.20E-03

Cell organization and biogenesis

221

12.20

4.40E-03

Cellular localization

101

5.60

4.50E-03

Protein localization

91

5.00

4.60E-03

Heterophilic cell adhesion

6

0.30

4.70E-03

Proteolysis

129

7.10

5.20E-03

Establishment of cellular localization

100

5.50

5.70E-03

Oxygen and reactive oxygen species metabolism

18

1.00

6.20E-03

Sulfur metabolism

15

0.80

7.00E-03

Generation of precursor metabolites and energy

92

5.10

7.50E-03

Cellular metabolism

711

39.30

7.70E-03

Neurotransmitter secretion

23

1.30

8.00E-03

Regulated secretory pathway

23

1.30

8.00E-03

mRNA export from nucleus

7

0.40

8.40E-03

Establishment of protein localization

82

4.50

8.90E-03

Sterol metabolism

10

0.60

9.00E-03

Macromolecule metabolism

498

27.50

9.70E-03

Chromosome condensation

9

0.50

1.00E-02

Nuclear transport

16

0.90

1.00E-02

Molecular function

Catalytic activity

639

35.30

3.60E-10

Monooxygenase activity

38

2.10

1.50E-07

Oxidoreductase activity

131

7.20

1.40E-06

Protein binding

693

38.30

2.60E-06

Transporter activity

208

11.50

1.40E-05

Electron transporter activity

49

2.70

9.40E-05

Hydrolase activity

294

16.20

2.70E-04

Sequence-specific DNA binding

12

0.70

4.40E-04

Tetrapyrrole binding

16

0.90

1.30E-03

Heme binding

16

0.90

1.30E-03

Binding

990

54.70

1.80E-03

Carbon-carbon lyase activity

14

0.80

2.60E-03

Electrochemical potential-driven transporter activity

43

2.40

2.80E-03

Porter activity

43

2.40

2.80E-03

Calmodulin binding

18

1.00

3.60E-03

Carbohydrate transporter activity

19

1.00

5.10E-03

Phosphoric monoester hydrolase activity

36

2.00

6.50E-03

DNA-directed DNA polymerase activity

10

0.60

6.60E-03

Sugar porter activity

12

0.70

7.40E-03

Glutathione transferase activity

11

0.60

8.70E-03

Sugar transporter activity

13

0.70

1.00E-02

Cellular component

Microsome

31

1.70

5.80E-10

Vesicular fraction

31

1.70

5.80E-10

Cell fraction

34

1.90

1.20E-09

Membrane fraction

33

1.80

2.10E-09

Clathrin coat

9

0.50

3.80E-04

Replication fork

9

0.50

3.80E-04

Coated membrane

11

0.60

6.70E-04

Membrane coat

11

0.60

6.70E-04

Clathrin vesicle coat

8

0.40

1.10E-03

Clathrin coated vesicle membrane

8

0.40

1.10E-03

Golgi apparatus

24

1.30

1.40E-03

Coated pit

5

0.30

1.50E-03

Cell

673

37.20

1.60E-03

Cytoplasmic vesicle membrane

10

0.60

1.70E-03

Vesicle coat

10

0.60

1.70E-03

Coated vesicle membrane

10

0.60

1.70E-03

Cytoplasm

239

13.20

2.90E-03

Membrane

295

16.30

3.00E-03

Plasma membrane

83

4.60

3.80E-03

Alpha DNA polymerase

4

0.20

4.30E-03

    Chromosome

40

2.20

5.00E-03


*Number of genes in the annotation category. Number of genes in the annotation category/total number of significant genes. P value from a modified Fisher exact test for enrichment of genes in an annotation category. The cross-classified factors in the 2 × 2 contingency tables are genes in the annotation category versus not in the annotation category, and significant genes versus all genes on the array.

Jordan et al. Genome Biology 2007 8:R172   doi:10.1186/gb-2007-8-8-r172

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