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CAPIH: A Web interface for comparative analyses and visualization of host-HIV protein-protein interactions

Fan-Kai Lin1, Chia-Lin Pan1, Jinn-Moon Yang3, Trees-Juen Chuang2* and Feng-Chi Chen134*

Author Affiliations

1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350 Taiwan, Republic of China

2 Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan, Republic of China

3 Department of Life Science, National Chiao-Tung University, Hsinchu, 300 Taiwan, Republic of China

4 Department of Dentistry, Chinese Medical University, Taichung, 404 Taiwan, Republic of China

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BMC Microbiology 2009, 9:164  doi:10.1186/1471-2180-9-164

Published: 12 August 2009

Abstract

Background

The Human Immunodeficiency Virus type one (HIV-1) is the major causing pathogen of the Acquired Immune Deficiency Syndrome (AIDS). A large number of HIV-1-related studies are based on three non-human model animals: chimpanzee, rhesus macaque, and mouse. However, the differences in host-HIV-1 interactions between human and these model organisms have remained unexplored.

Description

Here we present CAPIH (

    C
omparative
    A
nalysis of
    P
rotein
    I
nteractions for
    H
IV-1), the first web-based interface to provide comparative information between human and the three model organisms in the context of host-HIV-1 protein interactions. CAPIH identifies genetic changes that occur in HIV-1-interacting host proteins. In a total of 1,370 orthologous protein sets, CAPIH identifies ~86,000 amino acid substitutions, ~21,000 insertions/deletions, and ~33,000 potential post-translational modifications that occur only in one of the four compared species. CAPIH also provides an interactive interface to display the host-HIV-1 protein interaction networks, the presence/absence of orthologous proteins in the model organisms in the networks, the genetic changes that occur in the protein nodes, and the functional domains and potential protein interaction hot sites that may be affected by the genetic changes. The CAPIH interface is freely accessible at http://bioinfo-dbb.nhri.org.tw/capih webcite.

Conclusion

CAPIH exemplifies that large divergences exist in disease-associated proteins between human and the model animals. Since all of the newly developed medications must be tested in model animals before entering clinical trials, it is advisable that comparative analyses be performed to ensure proper translations of animal-based studies. In the case of AIDS, the host-HIV-1 protein interactions apparently have differed to a great extent among the compared species. An integrated protein network comparison among the four species will probably shed new lights on AIDS studies.