An experimentally derived confidence score for binary protein-protein interactions (original) (raw)

References

1. Barrios-Rodiles, M. et al. High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307, 1621–1625 (2005).
   Article CAS Google Scholar
2. von Mering, C. et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399–403 (2002).
   Article CAS Google Scholar
3. Yu, H. et al. High-quality binary protein interaction map of the yeast interactome network. Science 322, 104–110 (2008).
   Article CAS Google Scholar
4. Ge, H., Liu, Z., Church, G.M. & Vidal, M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29, 482–486 (2001).
   Article CAS Google Scholar
5. Ramani, A.K., Bunescu, R.C., Mooney, R.J. & Marcotte, E.M. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol. 6, R40 (2005).
   Article Google Scholar
6. Ramani, A.K. et al. A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol. Syst. Biol. 4, 180 (2008).
   Article Google Scholar
7. Chiang, T. et al. Coverage and error models of protein-protein interaction data by directed graph analysis. Genome Biol. 8, R186 (2007).
   Article Google Scholar
8. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569–4574 (2001).
   Article CAS Google Scholar
9. Sato, S. et al. A large-scale protein protein interaction analysis in Synechocystis sp. PCC6803. DNA Res. 14, 207–216 (2007).
   Article CAS Google Scholar
10. Gavin, A.C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006).
    Article CAS Google Scholar
11. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643 (2006).
    Article CAS Google Scholar
12. Han, J.D. et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88–93 (2004).
    Article CAS Google Scholar
13. Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540–543 (2004).
    Article CAS Google Scholar
14. Rual, J.F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178 (2005).
    Article CAS Google Scholar
15. Vidalain, P.O. et al. Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 32, 363–370 (2004).
    Article CAS Google Scholar
16. Walhout, A.J. & Vidal, M. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24, 297–306 (2001).
    Article CAS Google Scholar
17. Eyckerman, S. et al. Design and application of a cytokine-receptor-based interaction trap. Nat. Cell Biol. 3, 1114–1119 (2001).
    Article CAS Google Scholar
18. Nyfeler, B., Michnick, S.W. & Hauri, H.P. Capturing protein interactions in the secretory pathway of living cells. Proc. Natl. Acad. Sci. USA 102, 6350–6355 (2005).
    Article CAS Google Scholar
19. Ramachandran, N. et al. Next-generation high-density self-assembling functional protein arrays. Nat. Methods 5, 535–538 (2008).
    Article CAS Google Scholar
20. Venkatesan, K. et al. An empirical framework for binary interactome mapping. Nat. Methods advance online publication, 10.1038/nmeth.1280 (7 December 2008).
21. Bader, G.D., Betel, D. & Hogue, C.W. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248–250 (2003).
    Article CAS Google Scholar
22. Chatr-aryamontri, A. et al. MINT: the Molecular INTeraction database. Nucleic Acids Res. 35, D572–D574 (2007).
    Article CAS Google Scholar
23. Mishra, G.R. et al. Human protein reference database–2006 update. Nucleic Acids Res. 34, D411–D414 (2006).
    Article CAS Google Scholar
24. Pagel, P. et al. The MIPS mammalian protein-protein interaction database. Bioinformatics 21, 832–834 (2005).
    Article CAS Google Scholar
25. Salwinski, L. et al. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 32, D449–D451 (2004).
    Article CAS Google Scholar
26. Cusick, M.E. et al. Literature-curated protein interaction datasets. Nat. Methods (in the press).
27. Rual, J.F. et al. Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 14, 2128–2135 (2004).
    Article CAS Google Scholar
28. Ben-Hur, A. & Noble, W.S. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics 7 (suppl. 1), S2 (2006).
    Article Google Scholar
29. Qi, Y., Bar-Joseph, Z. & Klein-Seetharaman, J. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 63, 490–500 (2006).
    Article CAS Google Scholar
30. Vidal, M. et al. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA 93, 10315–10320 (1996).
    Article CAS Google Scholar
31. Lemmens, I. et al. Heteromeric MAPPIT: a novel strategy to study modification-dependent protein-protein interactions in mammalian cells. Nucleic Acids Res. 31, e75 (2003).
    Article Google Scholar
32. Lemmens, I., Lievens, S., Eyckerman, S. & Tavernier, J. Reverse MAPPIT detects disruptors of protein-protein interactions in human cells. Nat. Protoc. 1, 92–97 (2006).
    Article CAS Google Scholar

Download references

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).

Author information

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

Authors

1. Pascal Braun
   You can also search for this author inPubMed Google Scholar
2. Murat Tasan
   You can also search for this author inPubMed Google Scholar
3. Matija Dreze
   You can also search for this author inPubMed Google Scholar
4. Miriam Barrios-Rodiles
   You can also search for this author inPubMed Google Scholar
5. Irma Lemmens
   You can also search for this author inPubMed Google Scholar
6. Haiyuan Yu
   You can also search for this author inPubMed Google Scholar
7. Julie M Sahalie
   You can also search for this author inPubMed Google Scholar
8. Ryan R Murray
   You can also search for this author inPubMed Google Scholar
9. Luba Roncari
   You can also search for this author inPubMed Google Scholar
10. Anne-Sophie de Smet
    You can also search for this author inPubMed Google Scholar
11. Kavitha Venkatesan
    You can also search for this author inPubMed Google Scholar
12. Jean-François Rual
    You can also search for this author inPubMed Google Scholar
13. Jean Vandenhaute
    You can also search for this author inPubMed Google Scholar
14. Michael E Cusick
    You can also search for this author inPubMed Google Scholar
15. Tony Pawson
    You can also search for this author inPubMed Google Scholar
16. David E Hill
    You can also search for this author inPubMed Google Scholar
17. Jan Tavernier
    You can also search for this author inPubMed Google Scholar
18. Jeffrey L Wrana
    You can also search for this author inPubMed Google Scholar
19. Frederick P Roth
    You can also search for this author inPubMed Google Scholar
20. Marc Vidal
    You can also search for this author inPubMed Google Scholar

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 toPascal Braun, Jan Tavernier, Jeffrey L Wrana, Frederick P Roth or Marc Vidal.

Supplementary information

Rights and permissions

About this article

Cite this article

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

Download citation

• Received: 04 June 2008
• Accepted: 17 November 2008
• Published: 07 December 2008
• Issue Date: January 2009
• DOI: https://doi.org/10.1038/nmeth.1281