GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data
Open accessAbstract
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.
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Virus-centric repositories have been established, including ViralZone and VirusMINT, and GPS-Prot focuses on HIV-host interactions.
“Virus-centric repositories have also been established, including ViralZone(97) and VirusMINT (98), as well as GPS-Prot, which focuses on HIV-host interactions (99).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [99]
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- Authors
- Fahey, M. E., Bennett, M. J., Mahon, C., Jäger, S., Pache, L., Kumar, D., Shapiro, A., Rao, K., Chanda, S. K., Craik, C. S., Frankel, A. D., & Krogan, N. J.
- Affiliations
- University of California, San Francisco (US)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- International Centre for Genetic Engineering and Biotechnology (IN)
- Corresponding author
- Frankel, Alan D
- Krogan, Nevan J
- ORCID
- Venue
- BMC Bioinformatics
- Published
- 2011-07-22
- Volume
- 12
- Issue
- 1
- Pages
- 298-298
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC3213248
- OpenAlex
- W1981990581
- Cited by
- 87
- References
- 68
- Citations by year
- 2025: 4 · 2024: 10 · 2023: 13 · 2022: 14 · 2021: 9 · 2020: 6 · 2019: 7 · 2018: 3 · 2017: 2 · 2016: 2 · 2015: 5 · 2014: 3 · 2013: 4 · 2012: 4
- FWCI
- 1.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health
- University of California, San Francisco
- National Institute of General Medical Sciences (P50GM082250, P50 GM82250)
- National Institute of Allergy and Infectious Diseases (P01AI090935)
- National Center for Research Resources (P41RR001614)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › Complex Network Analysis Techniques
- Keywords
- protein-protein interaction, genetic interactions, web-based visualization, network integration, protein complexes, functional modules, BioGRID, Mentha, HPRD
- MeSH terms
- Humans, Software, User-Computer Interface, HIV-1, HIV Infections, Internet, Protein Interaction Mapping, Systems Biology, Host-Pathogen Interactions
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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