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apbc2011_HIV



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Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV 1 interception Xiaoning Qian 1 Byung Jun Yoon 2 1 Department 2 Department of Computer Science and Engineering University of South Florida Tampa FL USA of Electrical and Computer Engineering Texas A M University College Station TX USA Email Xiaoning Qian xqian cse usf edu Byung Jun Yoon bjyoon ece tamu edu Corresponding author Abstract Background Human immunodeficiency virus type one HIV 1 is the major pathogen that causes the acquired immune deficiency syndrome AIDS With the availability of large scale protein protein interaction PPI measurements comparative network analysis can provide a promising way to study the host virus interactions and their functional significance in the pathogenesis of AIDS Until now there have been a large number of HIV studies based on various animal models In this paper we present a novel framework for studying the host HIV interactions through comparative network analysis across different species Results Based on the proposed framework we test our hypothesis that HIV 1 attacks essential biological pathways that are conserved across species We selected the Homo sapiens and Mus musculus PPI networks with the largest coverage among the PPI networks that are available from public databases By using a local network alignment algorithm based on hidden Markov models HMMs we first identified the pathways that are conserved in both networks Next we analyzed the HIV 1 susceptibility of these pathways in comparison with random pathways in the human PPI network Our analysis shows that the conserved pathways have a significantly higher probability of being intercepted by HIV 1 Furthermore Gene Ontology GO enrichment analysis shows that most of the enriched GO terms are related to signal transduction which has been conjectured to be one of the major mechanisms targeted by HIV 1 for the takeover of the host cell 1 Conclusions This proof of



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