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An experimentally derived confidence score for binary protein-protein interactions

Braun, Pascal and Tasan, Murat and Dreze, Matija and Barrios-Rodiles, Miriam and Lemmens, Irma and Yu, Haiyuan and Sahalie, Julie M and Murray, Ryan R and Roncari, Luba and de Smet, Anne-Sophie and Venkatesan, Kavitha and Rual, Jean-François and Vandenhaute, Jean and Cusick, Michael E and Pawson, Tony and Hill, David and Tavernier, Jan and Wrana, Jeffrey L and Roth, Frederick P and Vidal, Marc (2009) An experimentally derived confidence score for binary protein-protein interactions. Nature Methods, 6 (1). pp. 91-97. ISSN 1548-7105

Abstract

Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays. We benchmarked these assays against positive and random reference sets consisting of well documented pairs of interacting human proteins and randomly chosen protein pairs, respectively. A logistic regression model was trained using the data from these reference sets to combine the assay outputs and calculate the probability that any newly identified interaction pair is a true biophysical interaction once it has been tested in the tool kit. This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks.

Item Type: Article
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Additional Information: Author can archive post-print (ie final draft post-refereeing); Publisher's version/PDF cannot be used
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Date Deposited: 22 Feb 2010 11:50
Last Modified: 31 Jan 2013 00:52
URI: https://oak.novartis.com/id/eprint/1621

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