Table 1.
Data sources used to predict protein functional interactions
| Data source | Proteins | SwissProt proteins (coverage) | Interactions | Reference |
|---|---|---|---|---|
| Human PPIs | 10,287 | 10,029 (49%) | 53,743 | [45-47] |
| Fly PPIs | 13,383 | 4,088 (20%) | 939,639 (26,346a) | [45] |
| Worm PPIs | 5,223 | 1,477 (7%) | 122,192 (8,161a) | [45] |
| Yeast PPIs | 5,646 | 1,530 (8%) | 1,900,980 (167,574a) | [45] |
| Domain interaction | 60,569 | 15,218 (75%) | NA | [52] |
| Lee's Gene Expression | 8,250 | 7,647 (38%) | 206,117 | [49] |
| Prieto's Gene Expression | 3,024 | 2,901 (14%) | 13,441 | [50] |
| GO BP sharing | 14,197 | 14,197 (70%) | NA | [51] |
| PPIs from GeneWays | 5,252 | 5,252(26%) | 51,048 | [53] |
To calculate the coverage of SwissProt, we used 20,332, the total identifier number in SwissProt (UniProtKB/Swiss-Prot Release 56.9, 3 March 2009), as the denominator. The numbers of interactions from three model organisms have been mapped to human proteins based on Ensembl Compara [48] (see text for details). aNumbers of PPIs in the original species. BP, biological process.