Table 2

Enrichment of the most frequently classified gene functions

Description

BD genes

AD Genes

Same-pair interactions




Exp

Rand

P

Ratio

Exp

Rand

P

Ratio

Exp

Rand

P

Ratio


Protein modification

30

2.92

<0.00002

10.3

21

11.12

0.00210

1.9

25

14.86

0.09916

1.7

Cell cycle

22

1.27

<0.00002

17.3

19

4.83

<0.00002

3.9

26

4.40

0.00006

5.9

DNA metabolism

14

0.79

<0.00002

17.7

6

2.99

0.03006

2.0

6

1.15

0.00860

5.2

Transcription

9

2.04

0.00002

4.4

14

7.77

0.01134

1.8

7

1.85

0.00242

3.8

Gametogenesis

9

1.49

<0.00002

6.0

13

5.69

0.00172

2.3

7

1.53

0.00072

4.6

Neurogenesis

8

1.91

0.00018

4.2

12

7.29

0.03142

1.6

14

3.75

0.00168

3.7

Cell-surface receptor-linked signal transduction

8

2.48

0.00088

3.2

11

9.39

0.23272

1.2

5

3.05

0.12498

1.6

DNA repair

6

0.45

<0.00002

13.4

7

1.71

0.00030

4.1

3

0.28

0.00064

10.8

Intracellular signaling cascade

6

0.65

0.00002

9.3

6

2.44

0.01036

2.5

3

0.98

0.03602

3.1

Imaginal disk development

5

0.80

0.00022

6.3

9

3.04

0.00092

3.0

3

0.45

0.00266

6.7

Average

11.7

1.48

0.00022

9.2

11.8

5.63

0.03209

2.4

9.9

3.23

0.02769

4.71


The top 10 most frequently classified BD gene functions, derived from GO biological process level 4 (see Materials and methods), are shown. The number of proteins or pairs of proteins in our experimental data (Exp) with each GO function is shown, alongside the average number of times the function would appear in a random interaction map (Rand) having the same topology and number of proteins (see Materials and methods), and the ratio of Exp/Rand. The functions listed are significantly enriched in the BD list, to P < 0.001, and most to P < 0.0003. Cell cycle, DNA metabolism and DNA repair (highlighted) are the three most proportionally enriched classifications in the BD list, These classes are also enriched for self-associations in the interaction list, with cell cycle and DNA metabolism around six- and fivefold enriched, while DNA repair is approximately 11-fold more self-associated than expected by chance. Of these three, DNA metabolism is not significantly enriched in the AD gene list (P > 0.03), while the other two classifications are approximately fourfold enriched. A complete list of all functions and function pairs found in the interaction data is in Additional data file 4.

Stanyon et al. Genome Biology 2004 5:R96   doi:10.1186/gb-2004-5-12-r96

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