Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks

Nadezhda T. Doncheva*, John H. Morris, Henrietta Holze, Rebecca Kirsch, Katerina C. Nastou, Yesid Cuesta-Astroz, Thomas Rattei, Damian Szklarczyk, Christian Von Mering, Lars J. Jensen

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

36 Citations (Scopus)
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Abstract

Biological networks are often used to represent complex biological systems, which can contain several types of entities. Analysis and visualization of such networks is supported by the Cytoscape software tool and its many apps. While earlier versions of stringApp focused on providing intraspecies protein-protein interactions from the STRING database, the new stringApp 2.0 greatly improves the support for heterogeneous networks. Here, we highlight new functionality that makes it possible to create networks that contain proteins and interactions from STRING as well as other biological entities and associations from other sources. We exemplify this by complementing a published SARS-CoV-2 interactome with interactions from STRING. We have also extended stringApp with new data and query functionality for protein-protein interactions between eukaryotic parasites and their hosts. We show how this can be used to retrieve and visualize a cross-species network for a malaria parasite, its host, and its vector. Finally, the latest stringApp version has an improved user interface, allows retrieval of both functional associations and physical interactions, and supports group-wise enrichment analysis of different parts of a network to aid biological interpretation. stringApp is freely available at https://apps.cytoscape.org/apps/stringapp.

Original languageEnglish
JournalJournal of Proteome Research
Volume22
Issue number2
Pages (from-to)637-646
ISSN1535-3893
DOIs
Publication statusPublished - 2022

Bibliographical note

Publisher Copyright:
© 2022 The Authors. Published by American Chemical Society.

Keywords

  • cross-species interactions
  • Cytoscape
  • enrichment analysis
  • heterogeneous networks
  • host-parasite
  • omics data
  • STRING
  • stringApp
  • virus-host

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