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.