Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

By Nadezhda T. Doncheva, J. H. Morris, Jan Gorodkin, Lars Juhl Jensen. bioRxiv, 2018

1,917 citations recorded by the source corpus.

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 dataset, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.

Subfields: Molecular Biology, Spectroscopy, Statistical and Nonlinear Physics

View Paper: https://www.semanticscholar.org/paper/e811d629209cdeb151f4eca8e643d082cfe3b706

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The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, methodology): “Apart from the website, the database can be queried directly from within Cytoscape (via a dedicated app) (30) and from within R (via a Bioconductor package) (31).”
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest (2022, methodology): “Apart from the website, scientists can access STRING via a dedicated Cytoscape plugin (52), as”