Global landscape of protein complexes in the yeast Saccharomyces cerevisiae (original) (raw)

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Acknowledgements

We thank M. Chow, N. Mohammad, C. Chung and V. Fong for their assistance with the creation of the web resources. We are grateful to J. van Helden and S. Brohée for sharing information on their comparison of clustering methods before publication. This research was supported by grants from Genome Canada and the Ontario Genomics Institute (to J.F.G. and A.E.), the Canadian Institutes of Health Research (to A.E., N.J.K., J.F.G., S.J.W., S.P. and C.J.I.), the National Cancer Institute of Canada with funds from the Canadian Cancer Society (to J.F.G.), the Howard Hughes Medical Institute (to J.S.W. and E.O.), the McLaughlin Centre for Molecular Medicine (to S.J.W. and S.P.), the Hospital for Sick Children (to J.M.P.-A.), the National Sciences and Engineering Research Council (to N.J.K., T.R.H. and A.E.) and the National Institutes of Health (to A.S., M.G., A.P. and H.Y.).

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Author notes

1. Nevan J. Krogan
   Present address: Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, 94143, USA
2. Nevan J. Krogan and Gerard Cagney: *These authors contributed equally to this work

Authors and Affiliations

1. Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Ontario, M5S 3E1, Toronto, Canada
   Nevan J. Krogan, Gerard Cagney, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Nira Datta, Aaron P. Tikuisis, Thanuja Punna, Michael Shales, Xin Zhang, Michael Davey, Mark D. Robinson, James E. Bray, Anthony Sheung, Atanas Lalev, Peter Wong, Andrei Starostine, Myra M. Canete, Shamanta Chandran, Robin Haw, Jennifer J. Rilstone, Kiran Gandi, Natalie J. Thompson, Gabe Musso, Peter St Onge, Shaun Ghanny, Mandy H. Y. Lam, Gareth Butland, C. James Ingles, Timothy R. Hughes, Andrew Emili & Jack F. Greenblatt
2. Department of Medical Genetics and Microbiology, University of Toronto, 1 Kings College Circle, Ontario, M5S 1A8, Toronto, Canada
   Nevan J. Krogan, Mandy H. Y. Lam, C. James Ingles, Timothy R. Hughes, Andrew Emili & Jack F. Greenblatt
3. Conway Institute, University College Dublin, Belfield, 4, Dublin, Ireland
   Gerard Cagney
4. Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, Connecticut, 06520, New Haven, USA
   Haiyuan Yu, Alberto Paccanaro & Mark Gerstein
5. Hospital for Sick Children, 555 University Avenue, Ontario, M4K 1X8, Toronto, Canada
   Shuye Pu, José M. Peregrín-Alvarez, James Vlasblom, Samuel Wu, Chris Orsi, John Parkinson & Shoshana J. Wodak
6. Affinium Pharmaceuticals, 100 University Avenue, Ontario, M5J 1V6, Toronto, Canada
   Bryan Beattie, Dawn P. Richards, Veronica Canadien & Frank Mena
7. Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, UCSF, Genentech Hall S472C, 600 16th St, California, 94143, San Francisco, USA
   Sean R. Collins & Jonathan S. Weissman
8. Comparative Genomics Laboratory, Nara Institute of Science and Technology 8916-5, Takayama, Nara, Ikoma, 630-0101, Japan
   Amin M. Altaf-Ul & Shigehiko Kanaya
9. Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Boulevard, Missouri, 63104, St Louis, USA
   Ali Shilatifard
10. Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Massachusetts, 02138, Cambridge, USA
    Erin O'Shea

Authors

1. Nevan J. Krogan
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2. Gerard Cagney
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3. Haiyuan Yu
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4. Gouqing Zhong
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5. Xinghua Guo
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6. Alexandr Ignatchenko
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7. Joyce Li
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8. Shuye Pu
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9. Nira Datta
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10. Aaron P. Tikuisis
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11. Thanuja Punna
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12. José M. Peregrín-Alvarez
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13. Michael Shales
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14. Xin Zhang
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15. Michael Davey
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16. Mark D. Robinson
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17. Alberto Paccanaro
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18. James E. Bray
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19. Anthony Sheung
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20. Bryan Beattie
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21. Dawn P. Richards
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22. Veronica Canadien
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23. Atanas Lalev
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24. Frank Mena
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25. Peter Wong
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26. Andrei Starostine
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27. Myra M. Canete
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28. James Vlasblom
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29. Samuel Wu
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30. Chris Orsi
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31. Sean R. Collins
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32. Shamanta Chandran
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33. Robin Haw
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34. Jennifer J. Rilstone
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35. Kiran Gandi
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36. Natalie J. Thompson
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37. Gabe Musso
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38. Peter St Onge
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39. Shaun Ghanny
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40. Mandy H. Y. Lam
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41. Gareth Butland
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42. Amin M. Altaf-Ul
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43. Shigehiko Kanaya
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44. Ali Shilatifard
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45. Erin O'Shea
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46. Jonathan S. Weissman
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47. C. James Ingles
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48. Timothy R. Hughes
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49. John Parkinson
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50. Mark Gerstein
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51. Shoshana J. Wodak
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52. Andrew Emili
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53. Jack F. Greenblatt
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Corresponding authors

Correspondence toAndrew Emili or Jack F. Greenblatt.

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Competing interests

Protein interaction information from this paper has been provided to the BioGRID database (http://thebiogrid.org), as well as the International Molecular Interaction Exchange consortium (IMEx, http://imex.sf.net) consisting of BIND, DIP, IntAct, MINT and Mpact (MIPS). Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains Supplementary Discussion and Supplementary Methpds on generating the interaction network, visualization, and quality assessment. (PDF 124 kb)

Supplementary Figures 1–5

Supplementary Figure 1 details the co-localization of MIPS, Gavin, Ho, Core, Extended Core datasets. Supplementary Figure 2 details the semantic similarity (GO biological processes) for all. Supplementary Figure 3 details the cytoscape view indicating comparison with MIPS. Supplementary Figure 4 details the essentiality versus conservation, degree of connectivity and betweenness. Supplementary Figure 5 details the IWR1 complex data. (PDF 2567 kb)

Supplementary Figure 6

Guide to the yeast interactome database (PDF 3394 kb)

Supplementary Table Legends

This file contains a detailed text guide to the contents of the Supplementary Tables. (PDF 63 kb)

Supplementary Tables 1–3

Supplementary Table 1 is a list of all the 4562 proteins whose purification was attempted. Supplementary Table 2 is a list of all the 2357 proteins whose purification was successful. Supplementary Table 3 is a list of 4087 proteins that were identified via MS. (XLS 379 kb)

Supplementary Tables 4–6

Supplementary Table 4 is a list of 71 proteins that were identified in more than 3% of all the successful protein purifications. Supplementary Table 5 is a list of 2357 protein-protein interactions in the intersection dataset. Supplementary Table 6 is a list of 5496 protein-protein interactions in the merged dataset. (XLS 804 kb)

Supplementary Tables 7, 8 and 10

Supplementary Table 7 is a list of 7123 protein-protein interactions in the core dataset. Supplementary Table 8 is a list of 14317 protein-protein interactions in the extended dataset. Supplementary Table 10 is a list of protein complexes and their component subunits as identified by the Markov Cluster Algorithm. (TXT 6809 kb)

Supplementary Table 9

Complete list of all the putative S. cerevisiae protein-protein interactions identified in this study. (XLS 2884 kb)

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Krogan, N., Cagney, G., Yu, H. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.Nature 440, 637–643 (2006). https://doi.org/10.1038/nature04670

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• Received: 20 December 2005
• Accepted: 23 February 2006
• Published: 22 March 2006
• Issue Date: 30 March 2006
• DOI: https://doi.org/10.1038/nature04670