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. 2015 Jan;43(Database issue):D566-70.
doi: 10.1093/nar/gku1126. Epub 2014 Nov 6.

HIV-1, human interaction database: current status and new features

Danso Ako-Adjei  1 , William Fu  2 , Craig Wallin  1 , Kenneth S Katz  1 , Guangfeng Song  1 , Dakshesh Darji  1 , J Rodney Brister  1 , Roger G Ptak  2 , Kim D Pruitt  3
Affiliations

HIV-1, human interaction database: current status and new features

Danso Ako-Adjei et al. Nucleic Acids Res. 2015 Jan.

Abstract

The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database', available through the National Library of Medicine at http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions, serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. Each HIV-1 human protein interaction can be retrieved without restriction by web-based downloads and ftp protocols and includes: Reference Sequence (RefSeq) protein accession numbers, National Center for Biotechnology Information Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. In addition to specific HIV-1 protein-human protein interactions, included are interaction effects upon HIV-1 replication resulting when individual human gene expression is blocked using siRNA. A total of 3142 human genes are described participating in 12,786 protein-protein interactions, along with 1316 replication interactions described for each of 1250 human genes identified using small interfering RNA (siRNA). Together the data identifies 4006 human genes involved in 14,102 interactions. With the inclusion of siRNA interactions we introduce a redesigned web interface to enhance viewing, filtering and downloading of the combined data set.

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Figures

Figure 1.
Figure 1.
NCBI Gene report of HIV-1 Interactions. If involved in a protein–protein or siRNA established interaction the report page for such a human gene includes a section entitled ‘HIV-1 Interactions’ shown here. (A) Interactions described by siRNA (‘Replication Interactions’). (B) Protein–protein interactions. In both cases a description of the interaction is displayed as well as a link to the publication(s) supporting the described interaction. Included is a link to the main site for the HIV-1 Interaction Database.
Figure 2.
Figure 2.
Filtering results while browsing. The ‘Filters’ section (A) allows users to choose criteria from three menus: (B) ‘HIV protein’, (C) ‘Protein interaction’ and (D) ‘Replication interaction’. In this example, the filtering results in presenting only protein interactions where the HIV interactant is ‘vif’ and the interaction with a product of each indicated human gene ‘disrupts’ an activity. Clicking on ‘more…’ on any listed interaction yields a popup menu (E) with details including the human protein product RefSeq accession, the full text interaction description and the PubMed ID(s). Also visible (middle right) are the ‘Download’ and ‘View NCBI Gene records’ selection buttons, described in the text.
See this image and copyright information in PMC

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