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

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsGPS-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.

Characterization of the Influence of Mediator Complex in HIV-1 Transcription

“…Here, we provide a detailed analysis of the role of MED subunits in HIV replication and specifically on viral transcription, demonstrating that Mediator complex is a relevant factor affecting HIV-1 replication. We have identified nine Mediator subunits whose depletion significantly affects HIV-1 replication confirming previous reports linking Mediator to HIV (11,34,35). We could not identify any association between HIV replication or transcription and MED proteins associated with the CDK8 module (34), but we could replicate the effect of four subunits that appeared in at least two siRNA screens before: MED6, MED7, MED14, and MED28 (Table 2).…”

“…A high number of cellular factors modulate HIV infection (1,33), including Mediator subunits that have been previously identified as potential hits in whole genome siRNA-based screenings (34). Here, we provide a detailed analysis of the role of MED subunits in HIV replication and specifically on viral transcription, demonstrating that Mediator complex is a relevant factor affecting HIV-1 replication.…”

Global landscape of HIV–human protein complexes

“…These human–human interactions helped to identify many host complexes, including several that have been previously characterized (see Supplementary Information for a detailed discussion of the HIV–human interaction data sets). Ultimately, all data will be accessible for searching and comparison to other HIV-related data sets using the web-based software GPS-PROT 21 (http://www.gpsprot.org/). …”

Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host–pathogen interaction space

“…In addition, it provides genetic variation data and predictions of phosphorylation and methylation sites. Another database, GPSprot, is a meta-database that allows graphical browsing of HIV-human interaction networks [38]. Where some of the aforementioned databases just collect the interaction data-sets, others curate data by hand like PHI-base or PIG.…”