TRANSFAC®: transcriptional regulation, from patterns to profiles

V Matys

E Fricke

R Geffers

E Gößling

A Kel+12 authors

^{BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany}^{Institut für Genetik-Biozentrum, Technische Universität Braunschweig, Spielmannstrasse. 7, D-38106 Braunschweig, Germany}^{Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig, Germany}

^{To whom correspondence should be addressed. Email:}ed.esaboib@amv

Received 2002 Sep 16; Revised 2002 Oct 11; Accepted 2002 Oct 27.

Abstract

The TRANSFAC® database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER® database on anatomical structures and developmental stages. The functionality of Match™, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match™ Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC® public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC® Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER® free download versions are available at http://www.biobase.de:8080/index.html.

Abstract

^{Only those entries were counted which have a factor from}Saccharomyces cerevisiae assigned.

ACKNOWLEDGEMENTS

We would like to thank all present and former members of BIOBASE GmbH and the AG Bioinformatics at the German Research Centre for Biotechnology (GBF) for contributing to this work in various ways. This work is supported in part by a grant of the European Commission (contract no. QLRI-CT-1999-01333) and two grants of the German Ministry of Education and Research (BMBF, grant no. 0312432 and 031U210B).

ACKNOWLEDGEMENTS

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