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Protein Bioinformatics pp 235–253Cite as

Functional Interaction Network Construction and Analysis for Disease Discovery

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1558))

Abstract

Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform. In this chapter, we describe the detailed procedures on how this functional interaction network is constructed by integrating multiple external data sources, extracting functional interactions from human curated pathway databases, building a machine learning classifier called a Naïve Bayesian Classifier, predicting interactions based on the trained Naïve Bayesian Classifier, and finally constructing the functional interaction database. We also provide an example on how to use ReactomeFIViz for performing network-based data analysis for a list of genes.

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Author information

Authors and Affiliations

  1. Informatics and Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, ON, Canada, M5G 0A3

    Guanming Wu & Robin Haw

  2. Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA

    Guanming Wu

Authors
  1. Guanming Wu
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  2. Robin Haw
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Corresponding author

Correspondence to Guanming Wu .

Editor information

Editors and Affiliations

  1. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA

    Cathy H. Wu

  2. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA

    Cecilia N. Arighi

  3. Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA

    Karen E. Ross

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Wu, G., Haw, R. (2017). Functional Interaction Network Construction and Analysis for Disease Discovery. In: Wu, C., Arighi, C., Ross, K. (eds) Protein Bioinformatics. Methods in Molecular Biology, vol 1558. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6783-4_11

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  • DOI: https://doi.org/10.1007/978-1-4939-6783-4_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6781-0

  • Online ISBN: 978-1-4939-6783-4

  • eBook Packages: Springer Protocols

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