Skip to main content
eScholarship
Open Access Publications from the University of California

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

  • Author(s): Fahey, Marie E
  • Bennett, Melanie J
  • Mahon, Cathal
  • Jäger, Stefanie
  • Pache, Lars
  • Kumar, Dhiraj
  • Shapiro, Alex
  • Rao, Kanury
  • Chanda, Sumit K
  • Craik, Charles S
  • Frankel, Alan D
  • Krogan, Nevan J
  • et al.
Abstract

Abstract Background The increasing availability of HIV-host interaction datasets, including both physical and genetic interactions, has created a need for software tools to integrate and visualize the data. Because these host-pathogen interactions are extensive and interactions between human proteins are found within many different databases, it is difficult to generate integrated HIV-human interaction networks. Results We have developed a web-based platform, termed GPS-Prot http://www.gpsprot.org, that allows for facile integration of different HIV interaction data types as well as inclusion of interactions between human proteins derived from publicly-available databases, including MINT, BioGRID and HPRD. The software has the ability to group proteins into functional modules or protein complexes, generating more intuitive network representations and also allows for the uploading of user-generated data. Conclusions GPS-Prot is a software tool that allows users to easily create comprehensive and integrated HIV-host networks. A major advantage of this platform compared to other visualization tools is its web-based format, which requires no software installation or data downloads. GPS-Prot allows novice users to quickly generate networks that combine both genetic and protein-protein interactions between HIV and its human host into a single representation. Ultimately, the platform is extendable to other host-pathogen systems.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
Current View