title: Co-clustering of biological networks and gene expression data.
abstract: BACKGROUND
  Large scale gene expression data are often analysed by clustering genes based on gene expression data alone, though a priori knowledge in the form of biological networks is available. The use of this additional information promises to improve exploratory analysis considerably.
  
  
  RESULTS
  We propose constructing a distance function which combines information from expression data and biological networks. Based on this function, we compute a joint clustering of genes and vertices of the network. This general approach is elaborated for metabolic networks. We define a graph distance function on such networks and combine it with a correlation-based distance function for gene expression measurements. A hierarchical clustering and an associated statistical measure is computed to arrive at a reasonable number of clusters. Our method is validated using expression data of the yeast diauxic shift. The resulting clusters are easily interpretable in terms of the biochemical network and the gene expression data and suggest that our method is able to automatically identify processes that are relevant under the measured conditions.
authors.affiliation: Institute for Algorithms and Scientific Computing (SCAI), Fraunhofer Gesellschaft, Schloss Birlinghoven, Sankt Augustin, 53754, Germany. Daniel.Hanisch@scai.fhg.de
authors.forename: Daniel
authors.initials: D
authors.lastname: Hanisch
authors.forename: Alexander
authors.initials: A
authors.lastname: Zien
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D008660:Metabolism / Q000502:physiology*; D008954:Models, Biological; D008957:Models, Genetic; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D029701:Saccharomyces cerevisiae Proteins