title: Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection.
abstract: Systems virology integrates host-directed approaches with molecular profiling to understand viral pathogenesis. Self-contained statistical approaches that combine expression profiles of genes with the available databases defining the genes involved in the pathways (gene-sets) have allowed characterization of predictive gene-signatures associated with outcome of the influenza virus (IV) infection. However, such enrichment techniques do not take into account interactions among pathways that are responsible for the IV infection pathogenesis. We investigate dendritic cell response to seasonal H1N1 influenza A/New Caledonia/20/1999 (NC) infection and infer the Boolean logic rules underlying the interaction network of ligand induced signaling pathways and transcription factors. The model reveals several novel regulatory modes and provides insights into mechanism of cross talk between NFκB and IRF mediated signaling. Additionally, the logic rule underlying the regulation of IL2 pathway that was predicted by the Boolean model was experimentally validated. Thus, the model developed in this paper integrates pathway analysis tools with the dynamic modeling approaches to reveal the regulation between signaling pathways and transcription factors using genome-wide transcriptional profiles measured upon influenza infection.
authors.affiliation: Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Anderson
authors.affiliation: Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA.
authors.forename: Marta L
authors.initials: ML
authors.lastname: DeDiego
authors.affiliation: Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Topham
authors.affiliation: Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA.
authors.forename: Juilee
authors.initials: J
authors.lastname: Thakar
mesh_terms: D000465:Algorithms; D016208:Databases, Factual; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype; D007251:Influenza, Human / Q000175:diagnosis*; D007376:Interleukin-2 / Q000378:metabolism; D008962:Models, Theoretical; D016328:NF-kappa B / Q000378:metabolism; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014773:Virology
chemical_list: D007376:Interleukin-2; D016328:NF-kappa B; D014157:Transcription Factors