Negative protein-protein interactions
Negative protein-protein interaction datasets are required for training and evaluation of interaction prediction methods, as well as validation of high-throughput interaction discovery experiments. We have derived datasets of protein pairs that were tested in large-scale two-hybrid screens but not seen to interact.
Reference
Trabuco LG, Betts MJ, and Russell RB. Negative protein-protein interaction datasets derived from large-scale two-hybrid experiments. Methods, In press.
Download
The negative protein-protein interaction datasets described in the reference above are available for download in the standard PSI-MI TAB 2.6 format (gzipped).
| Dataset | Organism | PMID | Download |
|---|---|---|---|
| Stelzl2005 | Homo sapiens | 16169070 | 241M |
| Giot2003 | Drosophila melanogaster | 14605208 | 1.6G |
| Li2004 | Caenorhabditis elegans | 14704431 | 226M |
| Simonis2009 | Caenorhabditis elegans | 19123269 | 101M |
| Uetz2000 | Saccharomyces cerevisiae | 10688190 | 112M |
| Ito2001core | Saccharomyces cerevisiae | 11283351 | 44M |
| LaCount2005 | Plasmodium falciparum | 16267556 | 47M |
| Titz2008 | Treponema pallidum | 18509523 | 20M |
| Parrish2007 | Campylobacter jejuni | 17615063 | 76M |
| Sato2007 | Synechocystis sp. PCC6803 | 18000013 | 134M |
For each negative interaction, the shortest path between the two proteins in the underlying two-hybrid interactome is given in column 15 (confidence score) following the format: shortestPath:2, shortestPath:3, etc. If there is no path connecting the two proteins in the underlying interactome, the confidence score is given as shortestPath:NA.
Contact
If you have any questions above the datasets above, please contact Rob Russell.