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  • Correspondence
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Response to Letter of Correspondence – Bastiaens et al.

Nature Biotechnology volume 33, pages 339–342 (2015)Cite this article

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Barzel and Barabási reply:

Bastiaens et al.1 raise several pertinent issues regarding the silencing method we proposed in ref. 2. They argue that the method is conceptually similar to modular response analysis (MRA)3,4,5 and that the use of correlation-based predictions as input for silencing generates symmetrizable network predictions, which prevents the inference of directionality. We agree that the principles that underpin the silencing method reported in our manuscript2 are similar to those used to derive MRA3,4,5 methods and regret that we did not cite the relevant literature, which we were unaware of at the time of publication. However, the main contribution in ref. 2 was that silencing, unlike MRA, is designed to improve correlation and mutual information–based predictions. These statistical similarity measures are frequently used in the context of link prediction6,7, and thus, a method that can enhance their predictive power is a useful contribution towards the mapping of regulatory interactions8,9,10.

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Figure 1: Silencing correlation– and relevance-based predictions.

Change history

  • 30 April 2015

    In the version of this article initially published, citations were given for Supplementary Software 1 and 2; these files have been removed from the website and the citations replaced by ones for figshare and GitHub (see supplementary information for explanation). The Software files have been available on figshare since publication and are now also available at GitHub (https://github.com/baruchbarzel/NatureBiotech-31-720), the link for which we have added to the paper. The changes have been made in the HTML and PDF versions of the article.

References

  1. Bastiaens, et al. Nat. Biotechnol. 33, 336–339 (2015).

    Article  CAS  Google Scholar 

  2. Barzel, B. & Barabási, A.-L. Nat. Biotechnol. 31, 720–725 (2013).

    Article  CAS  Google Scholar 

  3. Kholodenko, B.N. et al. Proc. Natl. Acad. Sci. USA 99, 12841–12846 (2002).

    Article  CAS  Google Scholar 

  4. Kholodenko, B.N. Nat. Cell Biol. 9, 247–249 (2007).

    Article  CAS  Google Scholar 

  5. Kholodenko, B.N., Yaffe, M.B. & Kolch, W. Sci. Signal. 5, re1 (2012).

    Article  Google Scholar 

  6. Marbach, D. et al. Nat. Methods 9, 796–804 (2012).

    Article  CAS  Google Scholar 

  7. Butte, A.J. & Kohane, I.S. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pacific Symposium on Biocomputing 5, 415–426 (2000).

    Google Scholar 

  8. Margolin, A.A. et al. BMC Bioinformatics 7, S7 (2006).

    Article  Google Scholar 

  9. Faith, J.J. et al. PLoS Biol. 5, 1 (2007).

    Article  Google Scholar 

  10. Feizi, S. et al. Nat. Biotechnol. 31, 726–733 (2013).

    Article  CAS  Google Scholar 

  11. Wright, S. J. Agric. Res. 20, 557–585 (1921).

    Google Scholar 

  12. Davis, J. & Goadrich, M. The relationship between Precision-Recall and ROC curves. in Proceeding of the 23rd International Conference on Machine Learning (ACM, Pittsburg, Pennsylvania, 2006).

    Google Scholar 

  13. Gulbahce, N. et al. PLoS Comput. Biol. 8, e1002531 (2012).

    Article  CAS  Google Scholar 

  14. Barzel, B. & Biham, O. Phys. Rev. E 80, 046104 (2009).

    Article  Google Scholar 

  15. Barzel, B. & Barabási, A.-L. Nat. Phys. 9, 673–681 (2013).

    Article  CAS  Google Scholar 

  16. Maslov, S. & Ispolatov, I. Proc. Natl. Acad. Sci. USA 104, 13655–13660 (2007).

    Article  CAS  Google Scholar 

  17. Maslov, S. & Ispolatov, I. New J. Phys. 9, 273–283 (2007).

    Article  Google Scholar 

  18. Yan, K.-K., Walker, D. & Maslov, S. Phys. Rev. Lett. 101, 268102 (2008).

    Article  Google Scholar 

  19. Kauffman, S. Physica A 340, 733–740 (2004).

    Article  CAS  Google Scholar 

  20. Furusawa, C. & Kaneko, K. Phys. Rev. Lett. 90, 088102 (2003).

    Article  Google Scholar 

  21. Lu, T. et al. BMC Bioinformatics 6, 37–49 (2005).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Center for Complex Network Research and Departments of Physics, Computer Science and Biology, Northeastern University, Boston, Massachusetts, USA

    Baruch Barzel & Albert-László Barabási

  2. Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA

    Baruch Barzel & Albert-László Barabási

  3. Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA

    Albert-László Barabási

Authors
  1. Baruch Barzel
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  2. Albert-László Barabási
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Correspondence to Albert-László Barabási.

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The authors declare no competing financial interests.

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Barzel, B., Barabási, AL. Response to Letter of Correspondence – Bastiaens et al.. Nat Biotechnol 33, 339–342 (2015). https://doi.org/10.1038/nbt.3184

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