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Nucleic Acids Research, 2002, Vol. 30, No. 1 332-334
© 2002 Oxford University Press

TRANSCompel®: a database on composite regulatory elements in eukaryotic genes

Olga V. Kel-Margoulis1,2,*, Alexander E. Kel1,2, Ingmar Reuter1, Igor V. Deineko2 and Edgar Wingender1,3

1BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany, 2Institute of Cytology and Genetics SB RAN, 10 Lavrentyev pr., 630090, Novosibirsk, Russia and 3AG Bioinformatik, Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig, Germany

Originating from COMPEL, the TRANSCompel® database emphasizes the key role of specific interactions between transcription factors binding to their target sites providing specific features of gene regulation in a particular cellular content. Composite regulatory elements contain two closely situated binding sites for distinct transcription factors and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor–DNA and factor–factor interactions contribute to the function of composite elements (CEs). Information about the structure of known CEs and specific gene regulation achieved through such CEs appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well. Each database entry corresponds to an individual CE within a particular gene and contains information about two binding sites, two corresponding transcription factors and experiments confirming cooperative action between transcription factors. The COMPEL database, equipped with the search and browse tools, is available at http://www.gene-regulation.com/pub/databases.html#transcompel. Moreover, we have developed the program CATCHTM for searching potential CEs in DNA sequences. It is freely available as CompelPatternSearch at http://compel.bionet.nsc.ru/FunSite/CompelPatternSearch.html.

* To whom correspondence should be addressed at present address: BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbuettel, Germany. Tel: +49 5331 858426; Fax: +49 5331 858470; Email: oke{at}biobase.de


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