title: Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection.
abstract: BACKGROUND
  The extraction of biological knowledge from genome-scale data sets requires its analysis in the context of additional biological information. The importance of integrating experimental data sets with molecular interaction networks has been recognized and applied to the study of model organisms, but its systematic application to the study of human disease has lagged behind due to the lack of tools for performing such integration.
  
  
  RESULTS
  We have developed techniques and software tools for simplifying and streamlining the process of integration of diverse experimental data types in molecular networks, as well as for the analysis of these networks. We applied these techniques to extract, from genomic expression data from Hepatitis C virus-infected liver tissue, potentially useful hypotheses related to the onset of this disease. Our integration of the expression data with large-scale molecular interaction networks and subsequent analyses identified molecular pathways that appear to be induced or repressed in the response to Hepatitis C viral infection.
  
  
  CONCLUSIONS
  The methods and tools we have implemented allow for the efficient dynamic integration and analysis of diverse data in a major human disease system. This integrated data set in turn enabled simple analyses to yield hypotheses related to the response to Hepatitis C viral infection.
authors.affiliation: Institute for Systems Biology, 1441 N, 34th Street, Seattle, WA 98103, USA. dreiss@systemsbiology.org
authors.forename: David J
authors.initials: DJ
authors.lastname: Reiss
authors.forename: Iliana
authors.initials: I
authors.lastname: Avila-Campillo
authors.forename: Vesteinn
authors.initials: V
authors.lastname: Thorsson
authors.forename: Benno
authors.initials: B
authors.lastname: Schwikowski
authors.forename: Timothy
authors.initials: T
authors.lastname: Galitski
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020869:Gene Expression Profiling; D016678:Genome; D016174:Hepacivirus / Q000378:metabolism; D006526:Hepatitis C / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D020407:Internet; D008099:Liver / Q000821:virology; D008954:Models, Biological; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome; D012984:Software
chemical_list: D020543:Proteome