title: CSB.DB: a comprehensive systems-biology database.
abstract: CONCLUSIONS
  The open access comprehensive systems-biology database (CSB.DB) presents the results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life's complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The central part of CSB.DB, which we describe in this applications note, is a set of co-response databases that currently focus on the three key model organisms, Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana. CSB.DB gives easy access to the results of large-scale co-response analyses, which are currently based exclusively on the publicly available compendia of transcript profiles. By scanning for the best co-responses among changing transcript levels, CSB.DB allows to infer hypotheses on the functional interaction of genes. These hypotheses are novel and not accessible through analysis of sequence homology. The database enables the search for pairs of genes and larger units of genes, which are under common transcriptional control. In addition, statistical tools are offered to the user, which allow validation and comparison of those co-responses that were discovered by gene queries performed on the currently available set of pre-selectable datasets.
  
  
  BACKGROUND
  All co-response databases can be accessed through the CSB.DB Web server (http://csbdb.mpimp-golm.mpg.de/).
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany. Steinhauser@mpimp-golm.mpg.de <Steinhauser@mpimp-golm.mpg.de>
authors.forename: Dirk
authors.initials: D
authors.lastname: Steinhauser
authors.forename: Björn
authors.initials: B
authors.lastname: Usadel
authors.forename: Alexander
authors.initials: A
authors.lastname: Luedemann
authors.forename: Oliver
authors.initials: O
authors.lastname: Thimm
authors.forename: Joachim
authors.initials: J
authors.lastname: Kopka
mesh_terms: D003628:Database Management Systems; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D049490:Systems Biology / Q000379:methods; D018511:Systems Integration; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors