IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0105833.html
   My bibliography  Save this article

Systematic Reverse Engineering of Network Topologies: A Case Study of Resettable Bistable Cellular Responses

Author

Listed:
  • Debasish Mondal
  • Edward Dougherty
  • Abhishek Mukhopadhyay
  • Adria Carbo
  • Guang Yao
  • Jianhua Xing

Abstract

A focused theme in systems biology is to uncover design principles of biological networks, that is, how specific network structures yield specific systems properties. For this purpose, we have previously developed a reverse engineering procedure to identify network topologies with high likelihood in generating desired systems properties. Our method searches the continuous parameter space of an assembly of network topologies, without enumerating individual network topologies separately as traditionally done in other reverse engineering procedures. Here we tested this CPSS (continuous parameter space search) method on a previously studied problem: the resettable bistability of an Rb-E2F gene network in regulating the quiescence-to-proliferation transition of mammalian cells. From a simplified Rb-E2F gene network, we identified network topologies responsible for generating resettable bistability. The CPSS-identified topologies are consistent with those reported in the previous study based on individual topology search (ITS), demonstrating the effectiveness of the CPSS approach. Since the CPSS and ITS searches are based on different mathematical formulations and different algorithms, the consistency of the results also helps cross-validate both approaches. A unique advantage of the CPSS approach lies in its applicability to biological networks with large numbers of nodes. To aid the application of the CPSS approach to the study of other biological systems, we have developed a computer package that is available in Information S1.

Suggested Citation

  • Debasish Mondal & Edward Dougherty & Abhishek Mukhopadhyay & Adria Carbo & Guang Yao & Jianhua Xing, 2014. "Systematic Reverse Engineering of Network Topologies: A Case Study of Resettable Bistable Cellular Responses," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-12, August.
    • Handle: RePEc:plo:pone00:0105833
    DOI: 10.1371/journal.pone.0105833
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105833
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0105833&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0105833?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Johannes Jaeger & Svetlana Surkova & Maxim Blagov & Hilde Janssens & David Kosman & Konstantin N. Kozlov & Manu & Ekaterina Myasnikova & Carlos E. Vanario-Alonso & Maria Samsonova & David H. Sharp & J, 2004. "Dynamic control of positional information in the early Drosophila embryo," Nature, Nature, vol. 430(6997), pages 368-371, July.
    2. Theodore J Perkins & Johannes Jaeger & John Reinitz & Leon Glass, 2006. "Reverse Engineering the Gap Gene Network of Drosophila melanogaster," PLOS Computational Biology, Public Library of Science, vol. 2(5), pages 1-12, May.
    3. Tian Hong & Jianhua Xing & Liwu Li & John J Tyson, 2011. "A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells," PLOS Computational Biology, Public Library of Science, vol. 7(7), pages 1-13, July.
    4. Jeffrey V Wong & Bochong Li & Lingchong You, 2012. "Tension and Robustness in Multitasking Cellular Networks," PLOS Computational Biology, Public Library of Science, vol. 8(4), pages 1-12, April.
    5. George von Dassow & Eli Meir & Edwin M. Munro & Garrett M. Odell, 2000. "The segment polarity network is a robust developmental module," Nature, Nature, vol. 406(6792), pages 188-192, July.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Kolja Becker & Eva Balsa-Canto & Damjan Cicin-Sain & Astrid Hoermann & Hilde Janssens & Julio R Banga & Johannes Jaeger, 2013. "Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster," PLOS Computational Biology, Public Library of Science, vol. 9(10), pages 1-16, October.
    2. Maksat Ashyraliyev & Ken Siggens & Hilde Janssens & Joke Blom & Michael Akam & Johannes Jaeger, 2009. "Gene Circuit Analysis of the Terminal Gap Gene huckebein," PLOS Computational Biology, Public Library of Science, vol. 5(10), pages 1-16, October.
    3. Stefano Ciliberti & Olivier C Martin & Andreas Wagner, 2007. "Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology," PLOS Computational Biology, Public Library of Science, vol. 3(2), pages 1-10, February.
    4. Carl Song & Hilary Phenix & Vida Abedi & Matthew Scott & Brian P Ingalls & Mads Kærn & Theodore J Perkins, 2010. "Estimating the Stochastic Bifurcation Structure of Cellular Networks," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-11, March.
    5. repec:plo:pbio00:1000049 is not listed on IDEAS
    6. Adel Dayarian & Madalena Chaves & Eduardo D Sontag & Anirvan M Sengupta, 2009. "Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks," PLOS Computational Biology, Public Library of Science, vol. 5(1), pages 1-12, January.
    7. repec:plo:pcbi00:1000184 is not listed on IDEAS
    8. Ronald Thenius & Michael Bodi & Thomas Schmickl & Karl Crailsheim, 2013. "Novel method of virtual embryogenesis for structuring Artificial Neural Network controllers," Mathematical and Computer Modelling of Dynamical Systems, Taylor & Francis Journals, vol. 19(4), pages 375-387.
    9. repec:plo:pcbi00:0030092 is not listed on IDEAS
    10. repec:plo:pcbi00:1004295 is not listed on IDEAS
    11. repec:plo:pcbi00:1002025 is not listed on IDEAS
    12. Cummings, F.W, 2004. "A model of morphogenesis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 339(3), pages 531-547.
    13. repec:plo:pcbi00:1006630 is not listed on IDEAS
    14. Robert Clewley, 2012. "Hybrid Models and Biological Model Reduction with PyDSTool," PLOS Computational Biology, Public Library of Science, vol. 8(8), pages 1-8, August.
    15. Ryan N Gutenkunst & Joshua J Waterfall & Fergal P Casey & Kevin S Brown & Christopher R Myers & James P Sethna, 2007. "Universally Sloppy Parameter Sensitivities in Systems Biology Models," PLOS Computational Biology, Public Library of Science, vol. 3(10), pages 1-8, October.
    16. Zeina Shreif & Vipul Periwal, 2014. "A Network Characteristic That Correlates Environmental and Genetic Robustness," PLOS Computational Biology, Public Library of Science, vol. 10(2), pages 1-23, February.
    17. repec:plo:pone00:0014624 is not listed on IDEAS
    18. Bernd Boehm & Henrik Westerberg & Gaja Lesnicar-Pucko & Sahdia Raja & Michael Rautschka & James Cotterell & Jim Swoger & James Sharpe, 2010. "The Role of Spatially Controlled Cell Proliferation in Limb Bud Morphogenesis," PLOS Biology, Public Library of Science, vol. 8(7), pages 1-21, July.
    19. Stradner, Jürgen & Thenius, Ronald & Zahadat, Payam & Hamann, Heiko & Crailsheim, Karl & Schmickl, Thomas, 2013. "Algorithmic requirements for swarm intelligence in differently coupled collective systems," Chaos, Solitons & Fractals, Elsevier, vol. 50(C), pages 100-114.
    20. Andreas Wagner, 2015. "Causal Drift, Robust Signaling, and Complex Disease," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-29, March.
    21. Manuel Cambón & Óscar Sánchez, 2022. "Thermodynamic Modelling of Transcriptional Control: A Sensitivity Analysis," Mathematics, MDPI, vol. 10(13), pages 1-18, June.
    22. Theinmozhi Arulraj & Debashis Barik, 2018. "Mathematical modeling identifies Lck as a potential mediator for PD-1 induced inhibition of early TCR signaling," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-23, October.
    23. repec:plo:pone00:0153738 is not listed on IDEAS
    24. David M Holloway & Alexander V Spirov, 2017. "Transcriptional bursting in Drosophila development: Stochastic dynamics of eve stripe 2 expression," PLOS ONE, Public Library of Science, vol. 12(4), pages 1-24, April.
    25. Theodore J Perkins & Johannes Jaeger & John Reinitz & Leon Glass, 2006. "Reverse Engineering the Gap Gene Network of Drosophila melanogaster," PLOS Computational Biology, Public Library of Science, vol. 2(5), pages 1-12, May.
    26. repec:plo:pbio00:2002439 is not listed on IDEAS
    27. Liang, Qiantong & Lo, Wing-Cheong, 2021. "Analysis of Th1/Th2 response pattern with Treg cell inhibition and stochastic effect," Chaos, Solitons & Fractals, Elsevier, vol. 153(P1).
    28. Guillermo Rodrigo & Santiago F Elena, 2011. "Structural Discrimination of Robustness in Transcriptional Feedforward Loops for Pattern Formation," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-7, February.
    29. Miles Miller & Marc Hafner & Eduardo Sontag & Noah Davidsohn & Sairam Subramanian & Priscilla E M Purnick & Douglas Lauffenburger & Ron Weiss, 2012. "Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-18, July.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0105833. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.