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Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks.

Nadezhda T Doncheva1, John H Morris2, Henrietta Holze1

  • 1Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.

Journal of Proteome Research
|December 13, 2022
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Summary
This summary is machine-generated.

The stringApp 2.0 tool enhances biological network analysis by integrating diverse data sources, enabling visualization of complex systems like host-parasite interactions. This improved functionality aids biological interpretation and discovery.

Keywords:
CytoscapeSTRINGcross-species interactionsenrichment analysisheterogeneous networkshost−parasiteomics datastringAppvirus−host

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Biological networks are crucial for understanding complex biological systems.
  • Cytoscape software and its apps facilitate network analysis and visualization.
  • Previous stringApp versions focused on intraspecies protein-protein interactions from STRING.

Purpose of the Study:

  • To introduce stringApp 2.0, enhancing support for heterogeneous biological networks.
  • To demonstrate the integration of STRING data with other biological entities and associations.
  • To extend functionality for cross-species interactions, particularly host-parasite relationships.

Main Methods:

  • stringApp 2.0 was developed to support heterogeneous networks.
  • Implemented new data and query functionalities for cross-species protein-protein interactions.
  • Integrated STRING database interactions with external biological data sources.
  • Enhanced user interface and added group-wise enrichment analysis.

Main Results:

  • stringApp 2.0 enables the creation of networks with diverse biological entities and associations.
  • Demonstrated successful integration of a SARS-CoV-2 interactome with STRING data.
  • Showcased retrieval and visualization of a cross-species network for malaria parasite, host, and vector.
  • Improved retrieval of both functional associations and physical interactions.

Conclusions:

  • stringApp 2.0 significantly advances biological network analysis by supporting heterogeneous data integration.
  • The enhanced tool facilitates the study of complex biological systems, including host-pathogen interactions.
  • stringApp 2.0 provides improved visualization and analytical capabilities for biological interpretation.