IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v449y2016icp192-199.html
   My bibliography  Save this article

No tradeoff between versatility and robustness in gene circuit motifs

Author

Listed:
  • Payne, Joshua L.

Abstract

Circuit motifs are small directed subgraphs that appear in real-world networks significantly more often than in randomized networks. In the Boolean model of gene circuits, most motifs are realized by multiple circuit genotypes. Each of a motif’s constituent circuit genotypes may have one or more functions, which are embodied in the expression patterns the circuit forms in response to specific initial conditions. Recent enumeration of a space of nearly 17 million three-gene circuit genotypes revealed that all circuit motifs have more than one function, with the number of functions per motif ranging from 12 to nearly 30,000. This indicates that some motifs are more functionally versatile than others. However, the individual circuit genotypes that constitute each motif are less robust to mutation if they have many functions, hinting that functionally versatile motifs may be less robust to mutation than motifs with few functions. Here, I explore the relationship between versatility and robustness in circuit motifs, demonstrating that functionally versatile motifs are robust to mutation despite the inherent tradeoff between versatility and robustness at the level of an individual circuit genotype.

Suggested Citation

  • Payne, Joshua L., 2016. "No tradeoff between versatility and robustness in gene circuit motifs," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 449(C), pages 192-199.
  • Handle: RePEc:eee:phsmap:v:449:y:2016:i:c:p:192-199
    DOI: 10.1016/j.physa.2015.12.065
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437115010936
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

    File URL: https://libkey.io/10.1016/j.physa.2015.12.065?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Unknown, 2005. "Forward," 2005 Conference: Slovenia in the EU - Challenges for Agriculture, Food Science and Rural Affairs, November 10-11, 2005, Moravske Toplice, Slovenia 183804, Slovenian Association of Agricultural Economists (DAES).
    2. Trevor R. Sorrells & Lauren N. Booth & Brian B. Tuch & Alexander D. Johnson, 2015. "Intersecting transcription networks constrain gene regulatory evolution," Nature, Nature, vol. 523(7560), pages 361-365, July.
    3. U. Alon & M. G. Surette & N. Barkai & S. Leibler, 1999. "Robustness in bacterial chemotaxis," Nature, Nature, vol. 397(6715), pages 168-171, January.
    4. Mark Isalan & Caroline Lemerle & Konstantinos Michalodimitrakis & Carsten Horn & Pedro Beltrao & Emanuele Raineri & Mireia Garriga-Canut & Luis Serrano, 2008. "Evolvability and hierarchy in rewired bacterial gene networks," Nature, Nature, vol. 452(7189), pages 840-845, April.
    5. Avraham E Mayo & Yaakov Setty & Seagull Shavit & Alon Zaslaver & Uri Alon, 2006. "Plasticity of the cis-Regulatory Input Function of a Gene," PLOS Biology, Public Library of Science, vol. 4(4), pages 1-1, March.
    6. 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.
    7. Qian Chen & Yang Liu & Steven Maere & Eunkyoung Lee & Gert Van Isterdael & Zidian Xie & Wei Xuan & Jessica Lucas & Valya Vassileva & Saeko Kitakura & Peter Marhavý & Krzysztof Wabnik & Niko Geldner & , 2015. "A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development," Nature Communications, Nature, vol. 6(1), pages 1-12, December.
    8. Gürol M. Süel & Jordi Garcia-Ojalvo & Louisa M. Liberman & Michael B. Elowitz, 2006. "An excitable gene regulatory circuit induces transient cellular differentiation," Nature, Nature, vol. 440(7083), pages 545-550, March.
    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. Javier Santos-Moreno & Eve Tasiudi & Hadiastri Kusumawardhani & Joerg Stelling & Yolanda Schaerli, 2023. "Robustness and innovation in synthetic genotype networks," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. 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.
    3. Shintaro Nagata & Macoto Kikuchi, 2020. "Emergence of cooperative bistability and robustness of gene regulatory networks," PLOS Computational Biology, Public Library of Science, vol. 16(6), pages 1-24, June.
    4. Tadamune Kaneko & Macoto Kikuchi, 2022. "Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution," PLOS Computational Biology, Public Library of Science, vol. 18(1), pages 1-20, January.
    5. Pilar Lopez-Llompart & G. Mathias Kondolf, 2016. "Encroachments in floodways of the Mississippi River and Tributaries Project," Natural Hazards: Journal of the International Society for the Prevention and Mitigation of Natural Hazards, Springer;International Society for the Prevention and Mitigation of Natural Hazards, vol. 81(1), pages 513-542, March.
    6. Michelle Sheran Sylvester, 2007. "The Career and Family Choices of Women: A Dynamic Analysis of Labor Force Participation, Schooling, Marriage and Fertility Decisions," Review of Economic Dynamics, Elsevier for the Society for Economic Dynamics, vol. 10(3), pages 367-399, July.
    7. DAVID M. BLAU & WILBERT van der KLAAUW, 2013. "What Determines Family Structure?," Economic Inquiry, Western Economic Association International, vol. 51(1), pages 579-604, January.
    8. Afanasyev, Dmitriy O. & Fedorova, Elena A. & Popov, Viktor U., 2015. "Fine structure of the price–demand relationship in the electricity market: Multi-scale correlation analysis," Energy Economics, Elsevier, vol. 51(C), pages 215-226.
    9. Peter Viggo Jakobsen, 2009. "Small States, Big Influence: The Overlooked Nordic Influence on the Civilian ESDP," Journal of Common Market Studies, Wiley Blackwell, vol. 47(1), pages 81-102, January.
    10. Billio, Monica & Casarin, Roberto & Osuntuyi, Anthony, 2016. "Efficient Gibbs sampling for Markov switching GARCH models," Computational Statistics & Data Analysis, Elsevier, vol. 100(C), pages 37-57.
    11. Jan Babecký & Fabrizio Coricelli & Roman Horváth, 2009. "Assessing Inflation Persistence: Micro Evidence on an Inflation Targeting Economy," Czech Journal of Economics and Finance (Finance a uver), Charles University Prague, Faculty of Social Sciences, vol. 59(2), pages 102-127, June.
    12. Lloyd, S. P., 2017. "Unconventional Monetary Policy and the Interest Rate Channel: Signalling and Portfolio Rebalancing," Cambridge Working Papers in Economics 1735, Faculty of Economics, University of Cambridge.
    13. Ichiro Fukunaga, 2007. "Imperfect Common Knowledge, Staggered Price Setting, and the Effects of Monetary Policy," Journal of Money, Credit and Banking, Blackwell Publishing, vol. 39(7), pages 1711-1739, October.
    14. Albertazzi, Ugo & Gambacorta, Leonardo, 2009. "Bank profitability and the business cycle," Journal of Financial Stability, Elsevier, vol. 5(4), pages 393-409, December.
    15. Beck, Thorsten & Demirgüç-Kunt, Asli & Merrouche, Ouarda, 2013. "Islamic vs. conventional banking: Business model, efficiency and stability," Journal of Banking & Finance, Elsevier, vol. 37(2), pages 433-447.
    16. Jinho Bae & Chang-Jin Kim & Dong Kim, 2012. "The evolution of the monetary policy regimes in the U.S," Empirical Economics, Springer, vol. 43(2), pages 617-649, October.
    17. McMahon, Rob, 2020. "Co-developing digital inclusion policy and programming with indigenous partners: Interventions from Canada," Internet Policy Review: Journal on Internet Regulation, Alexander von Humboldt Institute for Internet and Society (HIIG), Berlin, vol. 9(2), pages 1-26.
    18. George W. Evans & Seppo Honkapohja, 2009. "Robust Learning Stability with Operational Monetary Policy Rules," Central Banking, Analysis, and Economic Policies Book Series, in: Klaus Schmidt-Hebbel & Carl E. Walsh & Norman Loayza (Series Editor) & Klaus Schmidt-Hebbel (Series (ed.),Monetary Policy under Uncertainty and Learning, edition 1, volume 13, chapter 5, pages 145-170, Central Bank of Chile.
    19. Lehtonen, Heikki & Kujala, Sanna, 2007. "Climate change impacts on crop risks and agricultural production in Finland," 101st Seminar, July 5-6, 2007, Berlin Germany 9259, European Association of Agricultural Economists.
    20. Michael Pomerleano, 2011. "Developing Regional Financial Markets – the Case of East Asia," Chapters, in: Ulrich Volz (ed.), Regional Integration, Economic Development and Global Governance, chapter 9, Edward Elgar Publishing.

    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:eee:phsmap:v:449:y:2016:i:c:p:192-199. 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: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    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.