Table 3

Composition of the C. elegans superimposed network

Network

Links

Nodes

Supported links

Genetically supported links (A)

Genetically supported links (B)

Physically supported links

Coexpression supported links

Co-phenotype supported links


Superimposed network

75,283

7,825

929 (7.2)

NA

NA

NA

NA

NA

SGI

1,246

461

63 (2.0)

43 (1.6)

53 (1.8)

9 (5.6)

2 (9.0)

4 (5.9)*

Lehner

341

161

25 (5.5)

13 (10.8)

23 (7.3)

3 (22.7)

1 (17.9)

1 (30.3)

Fine genetic interactions

2,279

1,022

152 (4.6)

NA

48 (1.7)

61 (27.8)

23 (36.1)

22 (20.2)

Transposed SGA

7,527

426

66 (2.3)

5 (4.5)

5 (3.2)*

43 (2.2)

14 (3.0)

4 (1.3)*

Interolog

12,796

4,339

723 (9.9)

61 (27.8)

110 (4.8)

NA

577 (14.6)

42 (3.9)

C. elegans protein interaction

3,967

2,624

27 (3.7)

7 (10.6)

10 (4.2)

NA

13 (3.8)

5 (3.4)*

Eukaryotic coexpression

43,363

5,232

695 (11.8)

23 (36.1)

40 (7.2)

577 (14.6)

NA

84 (6.1)

C. elegans co-phenotype

8,862

913

153 (5.2)

22 (20.2)

30 (6.1)

42 (3.9)

84 (6.1)

NA


The supported links column gives the number of links supported by other data within the superimposed network. The fold-enrichment over the average number obtained from 1,000 randomly permuted superimposed networks (representation factor) is given in brackets. Genetically supported links (A) refers to the number of links supported by fine genetic analysis reported in WormBase (release 170). Genetically supported links (B) refers to the number of links supported by genetic interactions reported in WormBase (release 170), Lehner et al. [24] or SGI. Physically supported links refers to the number of links supported by eukaryotic physical interactions (interologs; see text for details). Coexpression-supported links refers to the number of links supported by eukaryotic mRNA coexpression analysis (see text for details). Co-phenotype-supported links refers to the number of links supported by C. elegans co-phenotype correlations (see text for details). Unless followed by an asterisk, P values of the representation factor < 10-4. NA, not applicable.

Byrne et al. Journal of Biology 2007 6:8   doi:10.1186/jbiol58

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