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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions
13:56

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Published on: July 18, 2013

GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.

Marie E Fahey1, Melanie J Bennett, Cathal Mahon

  • 1Department of Cellular and Molecular Pharmacology, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.

BMC Bioinformatics
|July 23, 2011
PubMed
Summary
This summary is machine-generated.

We created GPS-Prot, a web-based tool for integrating HIV-host interaction data. This platform simplifies the visualization of complex genetic and protein-protein interactions, aiding research into HIV.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Increasing HIV-host interaction data necessitates integrated visualization tools.
  • Challenges exist in consolidating diverse human protein interaction data from multiple databases.
  • Generating comprehensive HIV-human interaction networks is complex.

Purpose of the Study:

  • To develop a user-friendly platform for integrating and visualizing HIV-host interaction data.
  • To facilitate the creation of comprehensive HIV-human interaction networks.
  • To provide a tool for combining genetic and protein-protein interaction data.

Main Methods:

  • Development of a web-based platform, GPS-Prot (http://www.gpsprot.org).
  • Integration of various HIV interaction data types and human protein interactions from public databases (MINT, BioGRID, HPRD).
  • Implementation of functional module and protein complex grouping for intuitive network visualization.
  • Inclusion of functionality for uploading user-generated data.

Main Results:

  • GPS-Prot enables facile integration of diverse HIV interaction data.
  • The platform visualizes integrated HIV-human protein-protein and genetic interaction networks.
  • Functional modules and protein complexes can be grouped for clearer network representations.
  • User-generated data can be uploaded and incorporated into networks.

Conclusions:

  • GPS-Prot is a web-based software tool for creating integrated HIV-host networks.
  • Its key advantage is the web format, eliminating software installation needs.
  • Novice users can readily generate networks combining genetic and protein-protein interactions.
  • The platform is adaptable for other host-pathogen systems.