title: CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions.
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.
  
  
  METHODS
  Here we present CAPIH (Comparative Analysis of Protein Interactions for HIV-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 approximately 86,000 amino acid substitutions, approximately 21,000 insertions/deletions, and approximately 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350 Taiwan, Republic of China. fankailin@gmail.com
authors.forename: Fan-Kai
authors.initials: FK
authors.lastname: Lin
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Pan
authors.forename: Jinn-Moon
authors.initials: JM
authors.lastname: Yang
authors.forename: Trees-Juen
authors.initials: TJ
authors.lastname: Chuang
authors.forename: Feng-Chi
authors.initials: FC
authors.lastname: Chen
mesh_terms: D000818:Animals; D055028:Comparative Genomic Hybridization; D030562:Databases, Protein; D004195:Disease Models, Animal; D015658:HIV Infections / Q000235:genetics*; D015497:HIV-1 / Q000378:metabolism*; D006801:Humans; D020407:Internet; D025941:Protein Interaction Mapping / Q000379:methods*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D013045:Species Specificity; D014584:User-Computer Interface
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