Human immunodeficiency virus type 1, human protein interaction database at NCBI

Abstract

The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Protein Interaction Database', available through the National Library of Medicine at www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions, was created to catalog all interactions between HIV-1 and human proteins published in the peer-reviewed literature. The database serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. To facilitate this discovery approach, the following information for each HIV-1 human protein interaction is provided and can be retrieved without restriction by web-based downloads and ftp protocols: Reference Sequence (RefSeq) protein accession numbers, Entrez Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. Currently, 2589 unique HIV-1 to human protein interactions and 5135 brief descriptions of the interactions, with a total of 14,312 PMID references to the original articles reporting the interactions, are stored in this growing database. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the 'HIV-1 protein interactions' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication.

Figure 1.

Partial report page of HIV-1 Gag interactions with human proteins. (A) All or part of the interaction data available for an HIV-1 protein can be accessed using the drop down menus. (B) The interacting relationship between HIV-1 and human proteins is reported below the menus. The figure illustrates a query section to display all interactions catalogued for the HIV-1 Pr55 (Gag) protein. The display is sorted alphabetically by the interaction term. For example, the first two interactions shown are: (i) Pr55 (Gag) protein associates with ATP-binding cassette, sub-family E, member 1; and (ii) Pr55 (Gag) protein binds to adaptor-related protein complex 2, alpha 1 subunit isoform 1. (C) Further down, the display shows the association of HIV-1 matrix and p6 with the mitogen-activated protein kinase 1 (MAPK1). (D) The arrow points to the link for the Entrez Gene reports (the green ‘G’ icon).

Figure 2.

Partial Entrez Gene report page for MAPK1. (A) The report page includes a link to the ‘HIV-1 protein interactions’ section in the Table of Contents. (B) The ‘HIV-1 protein interactions’ section shows the interaction of MAPK1 with different HIV-1 proteins. (C) Summary descriptions of the interactions are provided. (D) The interactions and descriptions are linked to the supporting literature in PubMed.

Figure 3.

Distribution of interactions based on biological process Gene Ontology (GO) terms and individual HIV-1 proteins. The x-axis shows the individual HIV-1 structural proteins Gag, Pol and Env and their cleavage products, and the regulatory and accessory HIV-1 proteins, Tat, Rev, Nef, Vpu, Vpr and Vif. The y-axis displays the number of interacting human proteins. The various colors represent the biological process categories according to GO terms.