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Table 2 Gene Ontology mappings

From: Analysis and functional classification of transcripts from the nematode Meloidogyne incognita

(a) Biological process

Categories and subcategories

Representation

% Representation of total

Metabolism

 

133

  

75%

   

   Protein metabolism and modifications

  

57

  

32%

  

Protein modification

   

25

  

14%

 

Protein biosynthesis

   

15

  

8%

 

Protein degradation

   

14

  

8%

 

Protein folding

   

3

  

2%

 

Glycoprotein metabolism

   

1

  

1%

 

   Catabolism

  

24

  

13%

  

Protein degradation

   

14

  

8%

 

Glycolysis

   

8

  

4%

 

   Phosphate metabolism

  

23

  

13%

  

Kinase

   

19

  

11%

 

Phosphatase

   

4

  

2%

 

   Biosynthesis

  

17

  

10%

  

Protein biosynthesis

   

15

  

8%

 

   Electron transport

  

21

  

12%

  

   Nucleic acid metabolism

  

16

  

9%

  

Transcription

   

13

  

7%

 

RNA metabolism

   

2

  

1%

 

DNA metabolism

   

1

  

1%

 

   Carbohydrate metabolism

  

11

  

6%

  

Glycolysis

   

8

  

4%

 

   Amino acid and derivative metabolism

  

4

  

2%

  

   One-carbon compound metabolism

  

3

  

2%

  

   Oxygen and radical metabolism

  

3

  

2%

  

   Nitrogen metabolism

  

1

  

1%

  

   Secondary metabolism

  

1

  

1%

  

Transport

 

24

  

13%

   

   Ion transport (including channels)

  

8

  

4%

  

   Protein transport and trafficing

  

4

  

2%

  

   Amino acid transport

  

2

  

1%

  

Cell communication

 

21

  

12%

   

   Signal transduction

  

20

  

11%

  

Intracellular signaling cascade

   

14

  

8%

 

Cell surface receptor linked signal transduction

   

4

  

2%

 

   Response to external stimulus

  

1

  

1%

  

(b) Cellular component

Categories and subcategories

Representation

%Representation of total

Cell

79

   

81%

   

   Intracellular

 

62

   

64%

  

Cytoplasm

  

42

   

43%

 

Ribosome

   

29

   

30%

Cytoskeleton

   

5

   

5%

Mitochondria

   

5

   

5%

Proteasome

   

2

   

2%

Translation factor

   

1

   

1%

Nucleus

  

15

   

15%

 

Unspecified

  

3

    

3%

Plasma membrane

  

1

    

1%

   Membrane

 

22

   

23%

  

Unspecified

  

16

    

16%

Mitochondrial membrane

  

4

    

4%

Integral membrane

  

2

    

2%

Extracellular

15

   

15%

   

Unlocalized

3

   

3%

   

(c) Molecular function

Categories and subcategories

Representation

% Representation of total

Ligand binding / carrier

135

   

52%

   

Nucleic acid binding

 

44

   

17%

  

Nucleotide binding

 

40

   

15%

  

Calcium binding

 

22

   

8%

  

Protein binding

 

12

   

5%

  

Carbohydrate binding

 

7

   

3%

  

Electron transport

 

3

   

1%

  

Lipid binding

 

3

   

1%

  

Heavy metal binding

 

1

   

<1%

  

Oxygen binding

 

1

   

<1%

  

Oxygen transport

 

1

   

<1%

  

Enzyme

101

   

39%

   

Hydrolase

 

37

   

14%

  

Transferase

 

26

   

10%

  

Oxidoreductase

 

22

   

8%

  

Kinase

 

15

   

6%

  

Phosphatase

 

8

   

3%

  

Helicase

 

4

   

2%

  

Lyase

 

4

   

2%

  

Aldolase

 

2

   

1%

  

Ligase

 

2

   

1%

  

Isomerase

 

1

   

<1%

  

Monooxygenase

 

1

   

<1%

  

Transporter

14

   

5%

   

Channel/pore

 

5

   

2%

  

Carrier

 

4

   

2%

  

Intracellular transporter

 

3

   

1%

  

Ion transporter

 

3

   

1%

  

Oxygen transporter

 

1

   

<1%

  

Signal transducer

9

   

3%

   

Receptor

 

5

   

2%

  

Receptor signaling protein

 

3

   

1%

  

Structural molecule

5

   

2%

   

Enzyme regulator

4

   

2%

   

Cell adhesion

1

   

<1%

   

Motor

1

   

<1%

   

Transcriptional regulator

1

   

<1%

   
  1. (a) 178 clusters generated 336 multiple mappings. Percentage representation is based on 178. (b) 97 clusters generated 107 multiple mappings. Percentage representation is based on 97. (c) 261 clusters generated 321 multiple mappings. Percentage representation is based on 261.
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Genome Biology

ISSN: 1474-760X

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