Detecting overlapping protein complexes in protein-protein interaction networks

Journal name:
Nature Methods
Volume:
9,
Pages:
471–472
Year published:
DOI:
doi:10.1038/nmeth.1938
Received
Accepted
Published online

We introduce clustering with overlapping neighborhood expansion (ClusterONE), a method for detecting potentially overlapping protein complexes from protein-protein interaction data. ClusterONE-derived complexes for several yeast data sets showed better correspondence with reference complexes in the Munich Information Center for Protein Sequence (MIPS) catalog and complexes derived from the Saccharomyces Genome Database (SGD) than the results of seven popular methods. The results also showed a high extent of functional homogeneity.

References

  1. Enright, A.J., van Dongen, S. & Ouzounis, C.A. Nucleic Acids Res. 30, 15751584 (2002).
  2. King, A., Pržulj, N. & Jurisica, I. Bioinformatics 20, 30133020 (2004).
  3. Pu, S., Wong, J., Turner, B., Cho, E. & Wodak, S. Nucleic Acids Res. 37, 825831 (2009).
  4. Bader, G.D. & Hogue, C.W. BMC Bioinformatics 4, 2 (2003).
  5. Liu, G., Wong, L. & Chua, H.N. Bioinformatics 25, 18911897 (2009).
  6. Gavin, A. et al. Nature 440, 631636 (2006).
  7. Krogan, N. et al. Nature 440, 637643 (2006).
  8. Collins, S.R. et al. Mol. Cell. Proteomics 6, 439450 (2007).
  9. Stark, C. et al. Nucleic Acids Res. 34, D535D539 (2006).
  10. Frey, B.J. & Dueck, D. Science 315, 972976 (2007).
  11. Palla, G., Derényi, I., Farkas, I. & Vicsek, T. Nature 435, 814818 (2005).
  12. Macropol, K., Can, T. & Singh, A. BMC Bioinformatics 10, 283 (2009).
  13. Mewes, H.W. et al. Nucleic Acids Res. 32, D41D44 (2004).
  14. Brohée, S. & van Helden, J. BMC Bioinformatics 7, 488 (2006).
  15. Radicchi, F., Castellano, C., Cecconi, F., Loreto, V. & Parisi, D. Proc. Natl. Acad. Sci. USA 101, 26582663 (2004).
  16. Jansen, R. & Gerstein, M. Curr. Opin. Microbiol. 7, 535545 (2004).
  17. Jansen, R. et al. Science 302, 449453 (2003).
  18. Friedel, C.C., Krumsiek, J. & Zimmer, R. J. Comput. Biol. 16, 971987 (2009).
  19. Huh, W.-K.K. et al. Nature 425, 686691 (2003).
  20. Benjamini, Y. & Hochberg, Y. J. R. Stat. Soc. B 57, 289300 (1995).
  21. Hong, E. et al. Nucleic Acids Res. 36, D577D581 (2008).
  22. Ashburner, M. et al. Nat. Genet. 25, 2529 (2000).
  23. Dwight, S. et al. Nucleic Acids Res. 30, 6972 (2002).
  24. Shannon, P. et al. Genome Res. 13, 24982504 (2003).
  25. Krumsiek, J., Friedel, C.C. & Zimmer, R. Bioinformatics 24, 21152116 (2008).

Download references

Author information

Affiliations

  1. Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham, UK.

    • Tamás Nepusz &
    • Alberto Paccanaro
  2. Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA.

    • Haiyuan Yu

Contributions

T.N. and A.P. conceived the study. T.N. devised and implemented the algorithm and conducted benchmarks. H.Y. evaluated the biological relevance of the results. A.P. supervised the project. H.Y., T.N. and A.P. discussed the results and implications. A.P. and T.N. wrote the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

Author details

Supplementary information

PDF files

  1. Supplementary Text and Figures (1M)

    Supplementary Figures 1–8, Supplementary Tables 1–4, Supplementary Discussion

Zip files

  1. Supplementary Data 1 (541K)

    Input data files used in the benchmarks.

  2. Supplementary Data 2 (20K)

    Gold standard data files used in the benchmarks.

Additional data