title: Associations between HIV and human pathways revealed by protein-protein interactions and correlated gene expression profiles.
abstract: BACKGROUND
  AIDS is one of the most devastating diseases in human history. Decades of studies have revealed host factors required for HIV infection, indicating that HIV exploits host processes for its own purposes. HIV infection leads to AIDS as well as various comorbidities. The associations between HIV and human pathways and diseases may reveal non-obvious relationships between HIV and non-HIV-defining diseases.
  
  
  RESULTS
  Human biological pathways were evaluated and statistically compared against the presence of HIV host factor related genes. All of the obtained scores comparing HIV targeted genes and biological pathways were ranked. Different rank results based on overlapping genes, recovered virus-host interactions, co-expressed genes, and common interactions in human protein-protein interaction networks were obtained. Correlations between rankings suggested that these measures yielded diverse rankings. Rank combination of these ranks led to a final ranking of HIV-associated pathways, which revealed that HIV is associated with immune cell-related pathways and several cancer-related pathways. The proposed method is also applicable to the evaluation of associations between other pathogens and human pathways and diseases.
  
  
  CONCLUSIONS
  Our results suggest that HIV infection shares common molecular mechanisms with certain signaling pathways and cancers. Interference in apoptosis pathways and the long-term suppression of immune system functions by HIV infection might contribute to tumorigenesis. Relationships between HIV infection and human pathways of disease may aid in the identification of common drug targets for viral infections and other diseases.
authors.affiliation: Department of Medical Informatics, Tzu Chi University, Hualien, Taiwan.
authors.forename: Kuang-Chi
authors.initials: KC
authors.lastname: Chen
authors.forename: Tse-Yi
authors.initials: TY
authors.lastname: Wang
authors.forename: Chen-hsiung
authors.initials: CH
authors.lastname: Chan
mesh_terms: D017209:Apoptosis; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D015658:HIV Infections / Q000175:diagnosis* / Q000378:metabolism*; D006679:HIV Seropositivity / Q000378:metabolism; D015497:HIV-1 / Q000378:metabolism; D006801:Humans; D007107:Immune System; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D009369:Neoplasms / Q000150:complications / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods; D015398:Signal Transduction; D014777:Virus Diseases / Q000378:metabolism