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Using the clustered circular layout as an informative method for visualizing protein–protein interaction networks

Authors

  • David C. Y. Fung,

    Corresponding author
    1. School of Information Technologies, The University of Sydney, New South Wales, Australia
    • School of Biotechnology and Biomolecular Sciences, New South Wales Systems Biology Initiative, The University of New South Wales, New South Wales, 2052, Australia Fax: +612-9385-1483
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  • Marc R. Wilkins,

    1. School of Biotechnology and Biomolecular Sciences, New South Wales Systems Biology Initiative, The University of New South Wales, New South Wales, Australia
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  • David Hart,

    1. Axogenic Proprietary Limited, Australian Technology Park, Eveleigh, New South Wales, Australia
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  • Seok-Hee Hong

    1. School of Information Technologies, The University of Sydney, New South Wales, Australia
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Abstract

The force-directed layout is commonly used in computer-generated visualizations of protein–protein interaction networks. While it is good for providing a visual outline of the protein complexes and their interactions, it has two limitations when used as a visual analysis method. The first is poor reproducibility. Repeated running of the algorithm does not necessarily generate the same layout, therefore, demanding cognitive readaptation on the investigator's part. The second limitation is that it does not explicitly display complementary biological information, e.g. Gene Ontology, other than the protein names or gene symbols. Here, we present an alternative layout called the clustered circular layout. Using the human DNA replication protein–protein interaction network as a case study, we compared the two network layouts for their merits and limitations in supporting visual analysis.

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