title: Global modeling of transcriptional responses in interaction networks.
abstract: BACKGROUND
  Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms between tissues, and potentially as yet unknown processes. The same method can also be applied to cell-biological conditions in one or more tissues.
  
  
  RESULTS
  We introduce a novel approach for organism-wide discovery and analysis of transcriptional responses in interaction networks. The method searches for local, connected regions in a network that exhibit coordinated transcriptional response in a subset of tissues. Known interactions between genes are used to limit the search space and to guide the analysis. Validation on a human pathway network reveals physiologically coherent responses, functional relatedness between tissues and coordinated, context-specific regulation of the genes.
  
  
  BACKGROUND
  Implementation is freely available in R and Matlab at http://www.cis.hut.fi/projects/mi/software/NetResponse
authors.affiliation: Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, Aalto, Finland. leo.lahti@iki.fi
authors.forename: Leo
authors.initials: L
authors.lastname: Lahti
authors.forename: Juha E A
authors.initials: JE
authors.lastname: Knuuttila
authors.forename: Samuel
authors.initials: S
authors.lastname: Kaski
mesh_terms: D030541:Databases, Genetic; D053263:Gene Regulatory Networks / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D014158:Transcription, Genetic / Q000235:genetics*