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Modeling Structural Protein Interaction Networks for Betweenness Analysis

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Information Sciences and Systems 2014

Abstract

Protein–protein interactions are usually represented as interaction networks (graphs), where the proteins are represented as nodes and the connections between the interacting proteins are shown as edges. Proteins or interactions with high betweenness are considered as key connector members of the network. The interactions of a protein are dictated by its structure. In this study, we propose a new protein interaction network model taking structures of proteins into consideration. With this model, it is possible to reveal simultaneous and mutually exclusive interactions of a protein. Effect of mutually exclusive interactions on information flow in a network is studied with weighted edge betweenness analysis and it is observed that a total of 68 % of bottlenecks found in p53 pathway network differed from bottlenecks found via regular edge betweenness analysis. The new network model favored the proteins which have regulatory roles and take part in cell cycle and molecular functions like protein binding, transcription factor binding, and kinase activity.

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Acknowledgments

Deniz Demircioğlu is supported by a TÜBİTAK (The Scientific and Technological Research Council of Turkey) fellowship. This work has been partially supported by TÜBİTAK, Research Grant Number: 113E164.

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Authors and Affiliations

  1. Department of Computer Engineering, Koç University, Sariyer, 34450, İstanbul, Turkey

    Deniz Demircioğlu & Attila Gursoy

  2. Department of Chemical and Biological Engineering, Koç University, Sariyer, 34450, İstanbul, Turkey

    Özlem Keskin

Authors
  1. Deniz Demircioğlu
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  2. Özlem Keskin
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  3. Attila Gursoy
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Corresponding author

Correspondence to Attila Gursoy .

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Editors and Affiliations

  1. Polish Academy of Sciences, Gliwice, Poland

    Tadeusz Czachórski

  2. Imperial College London, London, United Kingdom

    Erol Gelenbe

  3. Imperial College London, London, United Kingdom

    Ricardo Lent

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© 2014 Springer International Publishing Switzerland

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Demircioğlu, D., Keskin, Ö., Gursoy, A. (2014). Modeling Structural Protein Interaction Networks for Betweenness Analysis. In: Czachórski, T., Gelenbe, E., Lent, R. (eds) Information Sciences and Systems 2014. Springer, Cham. https://doi.org/10.1007/978-3-319-09465-6_38

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  • DOI: https://doi.org/10.1007/978-3-319-09465-6_38

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-09464-9

  • Online ISBN: 978-3-319-09465-6

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