The open-access comprehensive systems-biology database (CSB.DB) presents 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, which 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 application note, is a set of co-response databases, which 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 inferring 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 allows validation and comparison of those co-responses, which were discovered by gene queries performed on the currently available set of pre-selectable datasets.
All co-response databases can be accessed through the CSB.DB web server (http://csbdb.mpimp-golm.mpg.de/).