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Construction of Functional Protein Networks Using Domain Profile Associations

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Protein-Protein Interaction Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2074))

Abstract

Proteins are major functional molecules that physically and functionally interact to carry out cellular processes. The physical interactions are generally mediated by domain-level interactions. Thus, novel protein-protein interactions can be predicted using various computational methods based on domain-domain interactions, using resolved structures of protein complexes. Functional protein interactions can be inferred based on shared domains between proteins, since proteins involved in the same biological processes tend to harbor common domains. We recently developed a method of inferring functional interactions between proteins using associations between their domain compositions, which can be represented as domain profiles. Since the method requires only protein domain annotations, it can be easily applied to any species with a sequenced genome. Here, we describe in detail the method of generating domain profiles for proteins and measuring the association between them to infer functional interactions between proteins. We also demonstrate that domain profile association can be used to successfully construct a large-scale functional network of human proteins.

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Acknowledgments

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean Government (MSIT) (NRF-2018M3C9A5064709, NRF-2018R1A5A2025079) to I.L.

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Authors and Affiliations

  1. Yonsei Biomedical Research Institute, Yonsei University College of Medicine, Seoul, South Korea

    Jung Eun Shim

  2. Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea

    Insuk Lee

Authors
  1. Jung Eun Shim
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  2. Insuk Lee
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Corresponding authors

Correspondence to Jung Eun Shim or Insuk Lee .

Editor information

Editors and Affiliations

  1. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Stefan Canzar

  2. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Francisca Rojas Ringeling

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Shim, J.E., Lee, I. (2020). Construction of Functional Protein Networks Using Domain Profile Associations. In: Canzar, S., Ringeling, F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9873-9_3

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9872-2

  • Online ISBN: 978-1-4939-9873-9

  • eBook Packages: Springer Protocols

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