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Protein-Protein Interaction Networks pp 125–134Cite as

Informed Use of Protein–Protein Interaction Data: A Focus on the Integrated Interactions Database (IID)

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

Abstract

Protein–protein interaction data is fundamental in molecular biology, and numerous online databases provide access to this data. However, the huge quantity, complexity, and variety of PPI data can be overwhelming, and rather than helping to address research problems, the data may add to their complexity and reduce interpretability. This protocol focuses on solutions for some of the main challenges of using PPI data, including accessing data, ensuring relevance by integrating useful annotations, and improving interpretability. While the issues are generic, we highlight how to perform such operations using Integrated Interactions Database (IID; http://ophid.utoronto.ca/iid).

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Acknowledgments

The work was supported in part by the Canada Research Chair Program (CRC #225404), Krembil Foundation, Ontario Research Fund (GL2-01-030 and #34876), Natural Sciences Research Council (NSERC #203475), Canada Foundation for Innovation (CFI #225404, #30865), and IBM.

Author information

Authors and Affiliations

  1. Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada

    Chiara Pastrello, Max Kotlyar & Igor Jurisica

  2. Krembil Research Institute, University Health Network, Toronto, ON, Canada

    Chiara Pastrello, Max Kotlyar & Igor Jurisica

  3. Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada

    Igor Jurisica

  4. Department of Computer Science, University of Toronto, Toronto, ON, Canada

    Igor Jurisica

  5. Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia

    Igor Jurisica

Authors
  1. Chiara Pastrello
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  2. Max Kotlyar
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  3. Igor Jurisica
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Corresponding author

Correspondence to Igor Jurisica .

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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Pastrello, C., Kotlyar, M., Jurisica, I. (2020). Informed Use of Protein–Protein Interaction Data: A Focus on the Integrated Interactions Database (IID). 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_10

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9872-2

  • Online ISBN: 978-1-4939-9873-9

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