IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0028606.html
   My bibliography  Save this article

Unraveling the Design Principle for Motif Organization in Signaling Networks

Author

Listed:
  • Samrat Chatterjee
  • Dhiraj Kumar

Abstract

Cellular signaling networks display complex architecture. Defining the design principle of this architecture is crucial for our understanding of various biological processes. Using a mathematical model for three-node feed-forward loops, we identify that the organization of motifs in specific manner within the network serves as an important regulator of signal processing. Further, incorporating a systemic stochastic perturbation to the model we could propose a possible design principle, for higher-order organization of motifs into larger networks in order to achieve specific biological output. The design principle was then verified in a large, complex human cancer signaling network. Further analysis permitted us to classify signaling nodes of the network into robust and vulnerable nodes as a result of higher order motif organization. We show that distribution of these nodes within the network at strategic locations then provides for the range of features displayed by the signaling network.

Suggested Citation

  • Samrat Chatterjee & Dhiraj Kumar, 2011. "Unraveling the Design Principle for Motif Organization in Signaling Networks," PLOS ONE, Public Library of Science, vol. 6(12), pages 1-9, December.
    • Handle: RePEc:plo:pone00:0028606
    DOI: 10.1371/journal.pone.0028606
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028606
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0028606&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0028606?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. Leland H. Hartwell & John J. Hopfield & Stanislas Leibler & Andrew W. Murray, 1999. "From molecular to modular cell biology," Nature, Nature, vol. 402(6761), pages 47-52, December.
    2. Liang Qiao & Robert B Nachbar & Ioannis G Kevrekidis & Stanislav Y Shvartsman, 2007. "Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling," PLOS Computational Biology, Public Library of Science, vol. 3(9), pages 1-8, September.
    3. Steven H. Strogatz, 2001. "Exploring complex networks," Nature, Nature, vol. 410(6825), pages 268-276, March.
    4. Julian Downward, 2001. "The ins and outs of signalling," Nature, Nature, vol. 411(6839), pages 759-762, June.
    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. Joshua S Weitz & Philip N Benfey & Ned S Wingreen, 2007. "Evolution, Interactions, and Biological Networks," PLOS Biology, Public Library of Science, vol. 5(1), pages 1-3, January.
    2. Alexander Rivkind & Hallel Schreier & Naama Brenner & Omri Barak, 2020. "Scale free topology as an effective feedback system," PLOS Computational Biology, Public Library of Science, vol. 16(5), pages 1-24, May.
    3. Anupam Saxena & Hod Lipson & Francisco J Valero-Cuevas, 2012. "Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation," PLOS Computational Biology, Public Library of Science, vol. 8(11), pages 1-17, November.
    4. Hütt, M.-Th. & Lüttge, U., 2005. "The interplay of synchronization and fluctuations reveals connectivity levels in networks of nonlinear oscillators," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 350(2), pages 207-226.
    5. Emerson, Isaac Arnold & Amala, Arumugam, 2017. "Protein contact maps: A binary depiction of protein 3D structures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 465(C), pages 782-791.
    6. Faedo, Nicolás & García-Violini, Demián & Ringwood, John V., 2021. "Controlling synchronization in a complex network of nonlinear oscillators via feedback linearisation and H∞-control," Chaos, Solitons & Fractals, Elsevier, vol. 144(C).
    7. Xiao‐Bing Hu & Hang Li & XiaoMei Guo & Pieter H. A. J. M. van Gelder & Peijun Shi, 2019. "Spatial Vulnerability of Network Systems under Spatially Local Hazards," Risk Analysis, John Wiley & Sons, vol. 39(1), pages 162-179, January.
    8. Ruiz Vargas, E. & Mitchell, D.G.V. & Greening, S.G. & Wahl, L.M., 2014. "Topology of whole-brain functional MRI networks: Improving the truncated scale-free model," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 405(C), pages 151-158.
    9. Igor Belykh & Mateusz Bocian & Alan R. Champneys & Kevin Daley & Russell Jeter & John H. G. Macdonald & Allan McRobie, 2021. "Emergence of the London Millennium Bridge instability without synchronisation," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    10. Berahmand, Kamal & Bouyer, Asgarali & Samadi, Negin, 2018. "A new centrality measure based on the negative and positive effects of clustering coefficient for identifying influential spreaders in complex networks," Chaos, Solitons & Fractals, Elsevier, vol. 110(C), pages 41-54.
    11. Zhang, Yun & Liu, Yongguo & Li, Jieting & Zhu, Jiajing & Yang, Changhong & Yang, Wen & Wen, Chuanbiao, 2020. "WOCDA: A whale optimization based community detection algorithm," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 539(C).
    12. Soh, Harold & Lim, Sonja & Zhang, Tianyou & Fu, Xiuju & Lee, Gary Kee Khoon & Hung, Terence Gih Guang & Di, Pan & Prakasam, Silvester & Wong, Limsoon, 2010. "Weighted complex network analysis of travel routes on the Singapore public transportation system," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(24), pages 5852-5863.
    13. Wang, Qingyun & Duan, Zhisheng & Chen, Guanrong & Feng, Zhaosheng, 2008. "Synchronization in a class of weighted complex networks with coupling delays," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(22), pages 5616-5622.
    14. De Montis, Andrea & Ganciu, Amedeo & Cabras, Matteo & Bardi, Antonietta & Mulas, Maurizio, 2019. "Comparative ecological network analysis: An application to Italy," Land Use Policy, Elsevier, vol. 81(C), pages 714-724.
    15. He, He & Yang, Bo & Hu, Xiaoming, 2016. "Exploring community structure in networks by consensus dynamics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 450(C), pages 342-353.
    16. T. Botmart & N. Yotha & P. Niamsup & W. Weera, 2017. "Hybrid Adaptive Pinning Control for Function Projective Synchronization of Delayed Neural Networks with Mixed Uncertain Couplings," Complexity, Hindawi, vol. 2017, pages 1-18, August.
    17. Sgrignoli, P. & Agliari, E. & Burioni, R. & Schianchi, A., 2015. "Instability and network effects in innovative markets," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 108(C), pages 260-271.
    18. Long Ma & Xiao Han & Zhesi Shen & Wen-Xu Wang & Zengru Di, 2015. "Efficient Reconstruction of Heterogeneous Networks from Time Series via Compressed Sensing," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-12, November.
    19. Wu, Tianyu & Huang, Xia & Chen, Xiangyong & Wang, Jing, 2020. "Sampled-data H∞ exponential synchronization for delayed semi-Markov jump CDNs: A looped-functional approach," Applied Mathematics and Computation, Elsevier, vol. 377(C).
    20. Liang’an Huo & Fan Ding & Chen Liu & Yingying Cheng, 2018. "Dynamical Analysis of Rumor Spreading Model considering Node Activity in Complex Networks," Complexity, Hindawi, vol. 2018, pages 1-10, November.

    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:pone00:0028606. 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.