IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0035531.html
   My bibliography  Save this article

Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks

Author

Listed:
  • Frank Emmert-Streib

Abstract

It has been generally acknowledged that the module structure of protein interaction networks plays a crucial role with respect to the functional understanding of these networks. In this paper, we study evolutionary aspects of the module structure of protein interaction networks, which forms a mesoscopic level of description with respect to the architectural principles of networks. The purpose of this paper is to investigate limitations of well known gene duplication models by showing that these models are lacking crucial structural features present in protein interaction networks on a mesoscopic scale. This observation reveals our incomplete understanding of the structural evolution of protein networks on the module level.

Suggested Citation

  • Frank Emmert-Streib, 2012. "Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-13, April.
    • Handle: RePEc:plo:pone00:0035531
    DOI: 10.1371/journal.pone.0035531
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035531
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0035531&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0035531?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. Gergely Palla & Imre Derényi & Illés Farkas & Tamás Vicsek, 2005. "Uncovering the overlapping community structure of complex networks in nature and society," Nature, Nature, vol. 435(7043), pages 814-818, June.
    2. Sergi Lozano & Alex Arenas & Angel Sánchez, 2008. "Mesoscopic Structure Conditions the Emergence of Cooperation on Social Networks," PLOS ONE, Public Library of Science, vol. 3(4), pages 1-9, April.
    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. Jorge Peña & Yannick Rochat, 2012. "Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-13, September.
    2. Lambiotte, R. & Panzarasa, P., 2009. "Communities, knowledge creation, and information diffusion," Journal of Informetrics, Elsevier, vol. 3(3), pages 180-190.
    3. Eustace, Justine & Wang, Xingyuan & Cui, Yaozu, 2015. "Community detection using local neighborhood in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 436(C), pages 665-677.
    4. 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.
    5. Zhang, Jianlei & Zhang, Chunyan & Chu, Tianguang, 2011. "The evolution of cooperation in spatial groups," Chaos, Solitons & Fractals, Elsevier, vol. 44(1), pages 131-136.
    6. Pirvu Daniela & Barbuceanu Mircea, 2016. "Recent Contributions Of The Statistical Physics In The Research Of Banking, Stock Exchange And Foreign Exchange Markets," Annals - Economy Series, Constantin Brancusi University, Faculty of Economics, vol. 2, pages 85-92, April.
    7. Daniel M. Ringel & Bernd Skiera, 2016. "Visualizing Asymmetric Competition Among More Than 1,000 Products Using Big Search Data," Marketing Science, INFORMS, vol. 35(3), pages 511-534, May.
    8. Yu, Shuo & Alqahtani, Fayez & Tolba, Amr & Lee, Ivan & Jia, Tao & Xia, Feng, 2022. "Collaborative Team Recognition: A Core Plus Extension Structure," Journal of Informetrics, Elsevier, vol. 16(4).
    9. Carattini, Stefano & Fankhauser, Sam & Gao, Jianjian & Gennaioli, Caterina & Panzarasa, Pietro, 2023. "What does network analysis teach us about international environmental cooperation?," Ecological Economics, Elsevier, vol. 205(C).
    10. Shang, Jiaxing & Liu, Lianchen & Li, Xin & Xie, Feng & Wu, Cheng, 2016. "Targeted revision: A learning-based approach for incremental community detection in dynamic networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 443(C), pages 70-85.
    11. Roth, Camille, 2007. "Empiricism for descriptive social network models," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 378(1), pages 53-58.
    12. Sitabhra Sinha, 2014. "The Importance of Community," Studies in Microeconomics, , vol. 2(1), pages 49-61, June.
    13. Ying Song & Zhiwen Zheng & Yunmei Shi & Bo Wang, 2023. "GLOD: The Local Greedy Expansion Method for Overlapping Community Detection in Dynamic Provenance Networks," Mathematics, MDPI, vol. 11(15), pages 1-16, July.
    14. Shiau, Wen-Lung & Dwivedi, Yogesh K. & Yang, Han Suan, 2017. "Co-citation and cluster analyses of extant literature on social networks," International Journal of Information Management, Elsevier, vol. 37(5), pages 390-399.
    15. Zhang, Zhiwei & Wang, Zhenyu, 2015. "Mining overlapping and hierarchical communities in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 421(C), pages 25-33.
    16. J. Sylvan Katz & Guillermo Armando Ronda-Pupo, 2019. "Cooperation, scale-invariance and complex innovation systems: a generalization," Scientometrics, Springer;Akadémiai Kiadó, vol. 121(2), pages 1045-1065, November.
    17. Masa Tsuchiya & Vincent Piras & Alessandro Giuliani & Masaru Tomita & Kumar Selvarajoo, 2010. "Collective Dynamics of Specific Gene Ensembles Crucial for Neutrophil Differentiation: The Existence of Genome Vehicles Revealed," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-10, August.
    18. Wu, Zhihao & Lin, Youfang & Wan, Huaiyu & Tian, Shengfeng & Hu, Keyun, 2012. "Efficient overlapping community detection in huge real-world networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(7), pages 2475-2490.
    19. Atieh Mirshahvalad & Johan Lindholm & Mattias Derlén & Martin Rosvall, 2012. "Significant Communities in Large Sparse Networks," PLOS ONE, Public Library of Science, vol. 7(3), pages 1-7, March.
    20. Nie, Yanyi & Li, Wenyao & Pan, Liming & Lin, Tao & Wang, Wei, 2022. "Markovian approach to tackle competing pathogens in simplicial complex," Applied Mathematics and Computation, Elsevier, vol. 417(C).

    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:pone00:0035531. 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.