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Bioinformatics Advance Access originally published online on July 9, 2004
Bioinformatics 2004 20(18):3647-3651; doi:10.1093/bioinformatics/bth398
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

CSB.DB: a comprehensive systems-biology database

Dirk Steinhauser *,{dagger}, Björn Usadel {dagger}, Alexander Luedemann , Oliver Thimm and Joachim Kopka

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany

Received on June 5, 2004; accepted on June 30, 2004
Advance Access Publication July 9, 2004

Summary: 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.

Availability: All co-response databases can be accessed through the CSB.DB Web server (http://csbdb.mpimp-golm.mpg.de/).

Contact: Steinhauser{at}mpimp-golm.mpg.de

* To whom correspondence should be addressed.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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