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Refining literature curated protein interactions using expert opinions
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Tastan, Oznur, Qi, Yanjun, Carbonell, Jaime G. and Klein-Seetharaman, Judith (2015) Refining literature curated protein interactions using expert opinions. In: Biocomputing 2015, Kohala Coast, Hawaii, USA, 4–8 Jan 2015. Published in: Proceedings of the Pacific Symposium pp. 318-329. doi:10.1142/9789814644730_0031
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Official URL: http://dx.doi.org/10.1142/9789814644730_0031
Abstract
The availability of high-quality physical interaction datasets is a prerequisite for system-level analysis of interactomes and supervised models to predict protein-protein interactions (PPIs). One source is literature-curated PPI databases in which pairwise associations of proteins published in the scientific literature are deposited. However, PPIs may not be clearly labelled as physical interactions affecting the quality of the entire dataset. In order to obtain a high-quality gold standard dataset for PPIs between human immunodeficiency virus (HIV-1) and its human host, we adopted a crowd-sourcing approach. We collected expert opinions and utilized an expectation-maximization based approach to estimate expert labeling quality. These estimates are used to infer the probability of a reported PPI actually being a direct physical interaction given the set of expert opinions. The effectiveness of our approach is demonstrated through synthetic data experiments and a high quality physical interaction network between HIV and human proteins is obtained. Since many literature-curated databases suffer from similar challenges, the framework described herein could be utilized in refining other databases. The curated data is available at http://www.cs.bilkent.edu.tr/~oznur.tastan/supp/psb2015/…
| Item Type: | Conference Item (Paper) | ||||
|---|---|---|---|---|---|
| Divisions: | Faculty of Medicine > Warwick Medical School > Biomedical Sciences Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine > Metabolic and Vascular Health (- until July 2016) Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine Faculty of Medicine > Warwick Medical School |
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| Journal or Publication Title: | Proceedings of the Pacific Symposium | ||||
| Book Title: | Biocomputing 2015 | ||||
| Official Date: | 2015 | ||||
| Dates: |
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| Page Range: | pp. 318-329 | ||||
| DOI: | 10.1142/9789814644730_0031 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Conference Paper Type: | Paper | ||||
| Title of Event: | Biocomputing 2015 | ||||
| Type of Event: | Conference | ||||
| Location of Event: | Kohala Coast, Hawaii, USA | ||||
| Date(s) of Event: | 4–8 Jan 2015 |
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