Cataloguing the HIV type 1 human protein interaction network

Ptak, R. G. et al. (2008) Cataloguing the HIV type 1 human protein interaction network. AIDS Research and Human Retroviruses, 24(12), pp. 1497-1502. (doi: 10.1089/aid.2008.0113) (PMID:19025396) (PMCID:PMC2655106)

Abstract

Although many interactions between HIV-1 and human proteins have been reported in the scientific literature, no publicly accessible source for efficiently reviewing this information was available. Therefore, a project was initiated in an attempt to catalogue all published interactions between HIV-1 and human proteins. HIV-related articles in PubMed were used to develop a database containing names, Entrez GeneIDs, and RefSeq protein accession numbers of interacting proteins. Furthermore, brief descriptions of the interactions, PubMed identification numbers of articles describing the interactions, and keywords for searching the interactions were incorporated. Over 100,000 articles were reviewed, resulting in the identification of 1448 human proteins that interact with HIV-1 comprising 2589 unique HIV-1-to-human protein interactions. Preliminary analysis of the extracted data indicates 32% were direct physical interactions (e.g., binding) and 68% were indirect interactions (e.g., upregulation through activation of signaling pathways). Interestingly, 37% of human proteins in the database were found to interact with more than one HIV-1 protein. For example, the signaling protein mitogen-activated protein kinase 1 has a surprising range of interactions with 10 different HIV-1 proteins. Moreover, large numbers of interactions were published for the HIV-1 regulatory protein Tat and envelope proteins: 30% and 33% of total interactions identified, respectively. The database is accessible at http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/ and is cross-linked to other National Center for Biotechnology Information databases and programs via Entrez Gene. This database represents a unique and continuously updated scientific resource for understanding HIV-1 replication and pathogenesis to assist in accelerating the development of effective therapeutic and vaccine interventions.

• Item Type: Articles
• Additional Information: R.G.P., W.F., and B.E.S.-B. were funded in whole with federal funds from the NIH, NIAID under Contracts N01-AI-05415 and N01-AI-70042, and wish to thank Dr. Roger Miller, Project Officer, DAIDS. J.E.D. was supported by a Wellcome Trust studentship and J.W.P by a BBSRC project grant (BB/C515412/1). M.N.R., K.S.K, D.R.M., and K.D.P. were supported by the Intramural Research Program of the NIH, National Library of Medicine.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Robertson, Professor David and Dickerson, Dr Jonathan
• Authors: 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., and Dieffenbach, C. W.
• College/School: College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing; College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: AIDS Research and Human Retroviruses
• Publisher: Mary Ann Liebert
• ISSN: 0889-2229
• ISSN (Online): 1931-8405
• Published Online: 22 November 2008