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An experimentally derived confidence score for binary protein-protein interactions

Nature Methods volume 6, pages 91–97 (2009)Cite this article

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.

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Figure 1: Strategy for deriving a confidence score for individual protein-protein interactions after high-throughput screening using data from several complementary follow-up interaction assays.
Figure 2: Schematic descriptions of complementary tool kit assays for binary protein interaction.
Figure 3: Evaluation of assay performance at different stringencies using hsPRS-v1 and hsRRS-v1.
Figure 4: Performance of assays against positive and random reference sets PRS and RRS.
Figure 5: Application of the integrated confidence score.

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Acknowledgements

We thank S. Michnick and N. Ramachandran for reagents and technical help for the PCA and wNAPPA assays, respectively. We thank A. Datti, T. Sun and F. Vizeacoumar from the SMART Robotics Facility at the Samuel Lunenfeld Research Institute for help with the automated version of LUMIER assay. We thank all members of the Vidal, Tavernier, Roth, and Wrana laboratories for helpful discussions, Agencourt Biosciences for sequencing assistance, and A. Bird and D. Maher for administrative assistance. This work was supported by contributions from the W.M. Keck Foundation awarded to M.V., F.P.R. and D.E.H.; by the Ellison Foundation awarded to M.V.; by Institute Sponsored Research funds from the Dana-Farber Cancer Institute Strategic Initiative awarded to M.V. and CCSB; by US National Institutes of Health grants 5P50HG004233 and 2R01HG001715 awarded to M.V., F.P.R. and D.E.H., R01 ES015728 awarded to M.V., 5U54CA112952 awarded to J. Nevins (M.V. subcontract), 5U01CA105423 awarded to S.H. Orkin (M.V. project), R01 HG003224 awarded to F.P.R. and F32 HG004098 awarded to M.T.; by a University of Ghent grant GOA12051401 and the Fonds Wetenschappelijk Onderzoek– Vlanderen (FWO-V) G.0031.06 awarded to J.T., by a postdoctoral fellowship from the FWO-V awarded to I.L.; and by a grant from Genome Canada and funds from the Ontario Genomics Institute awarded to J.L.W. M.V. is a Chercheur Qualifié Honoraire from the Fonds de la Recherche Scientifique (FRS-FNRS, French Community of Belgium).

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Author notes

  1. Kavitha Venkatesan & Jean-François Rual

    Present address: Present addresses: Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue Cambridge MA 02139 (K.V.) and Harvard Medical School, Department of Cell Biology, 240 Longwood Avenue, Boston, Massachusetts 02115, USA (J.-F.R.).,

  2. Pascal Braun, Murat Tasan and Matija Dreze: These authors contributed equally to this work.

Authors and Affiliations

  1. Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, 02115, Massachusetts, USA

    Pascal Braun, Matija Dreze, Haiyuan Yu, Julie M Sahalie, Ryan R Murray, Kavitha Venkatesan, Jean-François Rual, Michael E Cusick, David E Hill, Frederick P Roth & Marc Vidal

  2. Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, 02115, Massachusetts, USA

    Pascal Braun, Matija Dreze, Haiyuan Yu, Julie M Sahalie, Ryan R Murray, Kavitha Venkatesan, Jean-François Rual, Michael E Cusick, David E Hill & Marc Vidal

  3. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, 02115, Massachusetts, USA

    Murat Tasan & Frederick P Roth

  4. Facultés Universitaires Notre-Dame de la Paix, 61 Rue de Bruxelles, Namur, 5000, Belgium

    Matija Dreze & Jean Vandenhaute

  5. Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, M5G 1X5, Ontario

    Miriam Barrios-Rodiles, Luba Roncari, Tony Pawson & Jeffrey L Wrana

  6. Department of Medical Protein Research, and Department of Biochemistry, Flanders Institute for Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium

    Irma Lemmens, Anne-Sophie de Smet & Jan Tavernier

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  1. Pascal Braun
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Contributions

P.B., M.T. and M.D. coordinated experiments and data analysis. P.B., M.D., J.M.S., J.-F.R., R.R.M. and H.Y. performed high-throughput Gateway cloning. P.B., H.Y. and J.M.S. implemented, developed and analyzed wNAPPA and PCA experiments. J.-F.R., K.V. and M.E.C. established PRSv1.0 and RRS reference sets. I.L., A.-S. de S., J.T. and K.V. coordinated, performed and analyzed MAPPIT experiments. M.B.-R., L.R. and J.L.W. coordinated, performed and analyzed LUMIER experiments. M.T. and F.P.R. developed the regression model. M.V. conceived the project. M.V., T.P., J.L.W. and D.E.H. developed the concepts underlying the overall strategy. D.E.H., F.P.R. and M.V. co-directed the project.

Corresponding authors

Correspondence to Pascal Braun, Jan Tavernier, Jeffrey L Wrana, Frederick P Roth or Marc Vidal.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Table 1, Supplementary Data, Supplementary Methods, Supplementary Protocols 1–5 (PDF 2582 kb)

Supplementary Table 2

PM_IDs and full names for all hsPRS_v1 protein pairs (XLS 77 kb)

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Braun, P., Tasan, M., Dreze, M. et al. An experimentally derived confidence score for binary protein-protein interactions. Nat Methods 6, 91–97 (2009). https://doi.org/10.1038/nmeth.1281

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