HIV-1, Human Protein Interaction Database

Page Contents:

Interaction data results
Find related data in select NCBI databases
Project Overview
How to cite
Acknowledgements and contacts

Interaction data results:
Last updated: November 2007 to add data for env

The HIV-1, human protein interaction data presented here are based on literature reports. This dataset is available in report pages per HIV-1 protein and is also integrated into Entrez Gene report pages for HIV-1 and human proteins. The complete dataset is also available for FTP. [more...]

Reports & Downloads per HIV-1 protein:
env gag nef pol rev tat vif vpr vpu

Find Entrez Gene records that include HIV-1 interaction data:
By species: HIV-1 Human

Query Hints:

	Query	Description
	hiv1interactions[properties]	retrieve all Gene records that contain data compiled for this project
	hiv1interactions[properties] AND phenotype[properties]	retrieve the subset that also has associated phenotype data
	hiv1interactions[properties] AND gene_geo[filter]	retrieve the subset that also has gene expression data in the GEO database
	hiv1interactions[properties] AND gene_homologene[filter]	retrieve the subset that also has a HomoloGene cluster for the gene
	hiv1interactions[properties] AND transcription[go]	retrieve the subset that also has associated Gene Ontology (GO) terms for function, process, or component. The GO term "transcription" is used for this example.
	hiv1interactions[properties] AND kinase[domain name]	retrieve the subset that also has RefSeq proteins annotated with specific domain names. The domain name "kinase" is used for this example.
	hiv1interactions[properties] AND has_transcript_variants[properties]	retrieve the subset that also has >1 RefSeq transcript records for the gene
	hiv1interactions[properties] AND gene_pathways[filter]	retrieve the subset that also has information about biological pathways

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Find related data in select NCBI databases

Note: To identify new submissions, please use the Entrez "Limits" page. For example, select "30 days" from the menu entitled "Published in the last:". A range of date and other options are available.

Data type	Query	Description
Protein	"HIV-1"[organism] AND srcdb_refseq[properties]	HIV-1 reference sequence (RefSeq) proteins.
Protein	"HIV-1"[organism] NOT srcdb_refseq[properties]	HIV-1 protein records available in GenPept, excluding RefSeq records.
Structures	"HIV-1"[organism]	HIV-1 protein structure records. [Download Cn3D]
Nucleotide	NC_001802.1	HIV-1 reference sequence (RefSeq) genome.
Nucleotide	HIV-1[organism] NOT srcdb_refseq[properties]	HIV-1 nucleotide records that have become available in GenBank, excluding RefSeq records.
PopSets	HIV-1	HIV-1 population studies available in the Entrez PopSet database.
PubMed	HIV AND human AND protein AND interaction	Retrieve PubMed entries that may include reports of HIV-1, human protein interactions. Note this query is less restrictive to optimize finding more articles that may be relevent. Use the PubMed Limits settings to further restrict the query results by, for instance, restricting matches to terms found only in the title or abstract.
PubMed	HIV	Retrieve PubMed entries about HIV.

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Project Overview:

Documenting the interaction of human immunodeficiency virus type 1 (HIV-1) proteins with those of the host cell is crucial to understanding the process of HIV-1 replication and pathogenesis, and provides an essential foundation for the development of safe and effective therapeutic and prevention strategies to combat AIDS. Although numerous interactions have been reported in the scientific literature there is currently no publicly available source for efficiently accessing this information. Therefore, the Division of Acquired Immunodeficiency Syndrome (DAIDS) of the National Institute of Allergy and Infectious Diseases (NIAID) has initiated a project, in collaboration with Southern Research Institute and the National Center for Biotechnology Information (NCBI), designed to compile a comprehensive database of the described interactions between HIV-1 and cellular proteins.

The goal of this project is to provide scientists in the field of HIV/AIDS research a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. To this end, the database has been designed to track the following information for each protein-protein interaction identified in the literature:

NCBI Reference Sequence (RefSeq) protein accession numbers.
NCBI Entrez Gene ID numbers.
Amino acids from each protein that are known to be involved in the interaction.
Brief description of the protein-protein interaction.
Keywords to support searching for interactions.
National Library of Medicine (NLM) PubMed identification numbers (PMIDs) for all journal articles describing the interaction.

How to cite:

Please use these articles to cite use of the HIV-1, human protein interaction dataset and web resources:

Human immunodeficiency virus type 1, human protein interaction database at NCBI
Fu, W., Sanders-Beer, B.E., Katz, K.S., Maglott, D.R., Pruitt, K.D., Ptak, R.G.
Nucleic Acids Research 2009; 37(Database issue):D417-22
DOI: 10.1093/nar/gkn708; PDF, PubMed ID: 18927109

Cataloguing the HIV-1 Human Protein Interaction Network.
Ptak, R.G., Fu, W., Sanders-Beer, B.E., Dickerson, J.E., Pinney, J.W., Robertson, D.L.,
Rozanov, M.N., Katz, K.S., Maglott, D.R., Pruitt, K.D., Dieffenbach, C.W.
AIDS Research and Human Retroviruses 2008; 24(12):1497-502
DOI:10.1089/aid.2008.0113;PDF PubMed ID: 19025396 Supplemental Data (PDF) PubMed Central

HIV-host interactions: a map of viral perturbation of the host system.
Pinney, J.W.; Dickerson, J.E.; Fu, W.; Sanders-Beer, B.E.; Ptak, R.G.; Robertson, D.L.
AIDS 2009; 23(5):549-554.
DOI:10.1097/QAD.0b013e328325a495PubMed ID: 19262354

Acknowledgements and Contacts:

The initial review of the scientific literature and development of the database was performed by Mr. Roger Ptak, Dr. William Fu, and Dr. Brigitte Beer (Southern Research Institute, Frederick, Maryland). The work was supported by NIH contracts N01-AI-05415, Specialized In Vitro Virological Evaluations Of Strategies To Combat HIV/AIDS, and N01-AI-70042, In Vitro Testing Resources for AIDS Therapeutic Development Part B: Specialized In Vitro Virological Assays for HIV Therapeutics and Topical Microbicides, under direction of Dr. Roger Miller, Project Officer, DAIDS, NIAID. DAIDS gratefully acknowledges the efforts of Drs. Kim Pruitt, Donna Maglott, and Ken Katz (NCBI, NLM) for linking the database to NCBI programs and overseeing the updating of the database .

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