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Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

  • 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]
  • John H. Morris
    John H. Morris
    Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, California 94158-2517, United States
  • 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
  • , and 
  • 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]
Cite this: J. Proteome Res. 2019, 18, 2, 623–632
Publication Date (Web):November 19, 2018
https://doi.org/10.1021/acs.jproteome.8b00702
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.

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