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Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

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Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2019, 18, 2, 623-632
    Article

    Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data
    Click to copy article linkArticle link copied!

    • Nadezhda T. Doncheva*
      Nadezhda T. Doncheva
      Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
      Center for Non-Coding RNA in Technology and Health, University of Copenhagen, 1870 Frederiksberg C, Denmark
      Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
      *E-mail: [email protected]
      More by Nadezhda T. Doncheva
      Orcidhttp://orcid.org/0000-0002-8806-6850
    • John H. Morris
      John H. Morris
      Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, California 94158-2517, United States
      More by John H. Morris
      Orcidhttp://orcid.org/0000-0003-0290-7979
    • Jan Gorodkin
      Jan Gorodkin
      Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
      Center for Non-Coding RNA in Technology and Health, University of Copenhagen, 1870 Frederiksberg C, Denmark
      More by Jan Gorodkin
    • Lars J. Jensen*
      Lars J. Jensen
      Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
      Center for Non-Coding RNA in Technology and Health, University of Copenhagen, 1870 Frederiksberg C, Denmark
      *E-mail: [email protected]
      More by Lars J. Jensen
      Orcidhttp://orcid.org/0000-0001-7885-715X
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2019, 18, 2, 623–632
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    https://doi.org/10.1021/acs.jproteome.8b00702
    Published November 19, 2018
    Copyright © 2018 American Chemical Society
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    Abstract

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    Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import, and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics data set, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.

    Copyright © 2018 American Chemical Society

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jproteome.8b00702.

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    This article is cited by 1194 publications.

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    Cite this: J. Proteome Res. 2019, 18, 2, 623–632
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