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I2D - Interologous Interaction Database


NAR Molecular Biology Database Collection entry number 897
Brown K.R.1,2 and Jurisica I.1,2,3
1Ontario Cancer Institute, Toronto Medical Discoveries Tower, Life Sciences Discovery Centre, 101 College Street, Toronto, Ontario M5G 1L7
2Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
3Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

Database Description

High-throughput experiments are being performed at an ever-increasing rate to systematically elucidate protein-protein interaction (PPI) networks for model organisms, while similar experiments for human networks have lagged far behind. The Online Predicted Human Interaction Database (OPHID) is a web-based database of predicted interactions between human proteins. It combines the literature-derived human PPIs from BIND, HPRD and MINT, with predictions made from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Mus musculus. The 23,889 predicted interactions currently listed in OPHID are evaluated using protein domains, gene co-expression and Gene Ontology terms. OPHID can be queried using single IDs or batch queries, and using multiple supported ID types. The results can be displayed as text, HTML, or visualized using our custom graph visualization program. In addition, the entire database is available for download in tab-delimited text or PSI-compliant XML format.

Recent Developments

OPHID continues to expand in the number and type of interactions it contains. While the initial focus was on predictions, experimentally-verified human interactions have been growing in abundance. Recent data directly testing human proteins been added to the database, including datasets from Barrios-Rodiles et al., (PMID: 15761153), Rual et al., (PMID: 16189514), and Stelzl et al., (PMID: 16169070).

Acknowledgements

We acknowledge the hardware and software support from IBM Life Sciences through a Shared University Research Grant, and support from the National Science and Engineering Research Council, the Institute for Robotics and Intelligent Systems, Precarn Inc., Genome Canada, the Princess Margaret Hospital Foundation through funds raised by the Toronto Women's Fashion Show Committee and Younger Foundation.

References

1. Brown, K.R., and Jurisica, I. (2005) Online Predicted Human Interaction Database. Bioinformatics 21: 2076-2082.


Go to the abstract in Bioinformatics, 2005, 21, 2076-2082
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