Nucleic Acids Research Advance Access published online on May 14, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn292
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GeneCAT—novel webtools that combine BLAST and co-expression analyses
1Department of Molecular Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark and 2Max-Planck-Institute for Molecular Plant Physiology, Am Muehlenberg 2, 14476 Potsdam, Germany
*To whom correspondence should be addressed. Tel: +49 331 567 8149; Fax: +49 331 567 8408; Email: mutwil{at}mpimp-golm.mpg.de
Received January 3, 2008. Revised April 14, 2008. Accepted April 29, 2008.
The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughput Map-O-Matic tool matches co-expression pattern of multiple query genes to genes present in user-defined subdatabases, and can therefore be used for gene mapping in forward genetic screens. Third, Rosetta combines co-expression analysis with BLAST and can be used to find ‘true’ gene orthologs in the plant model organisms Arabidopsis thaliana and Hordeum vulgare (Barley). GeneCAT is equipped with expression data for the model plant A. thaliana, and first to introduce co-expression mining tools for the monocot Barley. GeneCAT is available at http://genecat.mpg.de