title: BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies.
abstract: BACKGROUND
  Understanding of immune response mechanisms of pathogen-infected host requires multi-scale analysis of genome-wide data. Data integration methods have proved useful to the study of biological processes in model organisms, but their systematic application to the study of host immune system response to a pathogen and human disease is still in the initial stage.
  
  
  RESULTS
  To study host-pathogen interaction on the systems biology level, an extension to the previously described BiologicalNetworks system is proposed. The developed methods and data integration and querying tools allow simplifying and streamlining the process of integration of diverse experimental data types, including molecular interactions and phylogenetic classifications, genomic sequences and protein structure information, gene expression and virulence data for pathogen-related studies. The data can be integrated from the databases and user's files for both public and private use.
  
  
  CONCLUSIONS
  The developed system can be used for the systems-level analysis of host-pathogen interactions, including host molecular pathways that are induced/repressed during the infections, co-expressed genes, and conserved transcription factor binding sites. Previously unknown to be associated with the influenza infection genes were identified and suggested for further investigation as potential drug targets. Developed methods and data are available through the Java application (from BiologicalNetworks program at http://www.biologicalnetworks.org) and web interface (at http://flu.sdsc.edu).
authors.affiliation: San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Kozhenkov
authors.forename: Mayya
authors.initials: M
authors.lastname: Sedova
authors.forename: Yulia
authors.initials: Y
authors.lastname: Dubinina
authors.forename: Amarnath
authors.initials: A
authors.lastname: Gupta
authors.forename: Animesh
authors.initials: A
authors.lastname: Ray
authors.forename: Julia
authors.initials: J
authors.lastname: Ponomarenko
authors.forename: Michael
authors.initials: M
authors.lastname: Baitaluk
mesh_terms: D000818:Animals; D000998:Antiviral Agents / Q000378:metabolism / Q000494:pharmacology / Q000627:therapeutic use; D057225:Data Mining; D016208:Databases, Factual; D054884:Host-Pathogen Interactions; D006801:Humans; D051379:Mice; D009975:Orthomyxoviridae / Q000187:drug effects / Q000502:physiology; D009976:Orthomyxoviridae Infections / Q000188:drug therapy / Q000378:metabolism; D058974:Phylogeography; D051381:Rats; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D000998:Antiviral Agents