Go to the abstract in the NAR 2003 Database Issue.
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http://www.biobase.de/pages/products/databases.html
Krull, M., Choi, C., Pistor, S., Voss, N., Wingender, E.
BIOBASE Biological Databases GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany
Contact mkl@biobase.de
TRANSPATH is a database system about gene regulatory networks that combines detailed information on signal transduction with tools for visualisation and analysis [1]. The integration with TRANSFAC, a database about transcription factors and their DNA binding sites [2], provides the possibility to obtain complete signalling pathways from ligand to target genes and their products, which may themselves be involved in regulatory action. As of July 2002, the TRANSPATH Professional release 3.2 contains about 9800 molecules, >1800 genes, and >11400 reactions collected from ~5000 references. The Molecule table describes proteins and other components such as small effectors (Ca2+ ions, NO) that transduce extracellular signals to target genes and specifies their intracellular and tissue-specific distribution. Gene contains information on target genes and gene expression as starting points for regulatory pathways or feedback loops. Reaction entries connect signalling molecules, give information on the interaction mechanism and effects, and constitute paths, pathways and networks [3]. All data have been manually extracted from peer-reviewed literature (except an initial molecule import from SwissProt release 3.6 (1129 entries)) and are curated by specialist annotators. The reliability of interaction data concerning their biological relevance is evaluated and a respective quality value is assigned. Cross-references to important sequence and signature databases such as EMBL/GenBank, SWISS-PROT, InterPro, or LocusLink are provided. With the ArrayAnalyzer(TM), an integrated tool has been developed for evaluation of microarray data. It uses the TRANSPATH data set to identify key regulators in pathways connected with up- or down-regulated genes of the respective array. The key molecules and their surrounding networks can be viewed with the PathwayBuilder(TM), a tool that offers four different modes of visualisation.
[1] Schacherer,F., Choi,C., Götze,U., Krull,M., Pistor,S. and Wingender,E. (2001)
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics 17, 1053-1057.
[2] Wingender,E., Chen,X., Fricke,E., Geffers,R., Hehl,R., Liebich,I., Krull,M., Matys,V., Michael,H., Ohnhäuser,R., Prüß,M., Schacherer,F., Thiele,S. and Urbach,S. (2001)
The TRANSFAC system on gene expression regulation.
Nucleic Acids Res. 29, 281-283.
[3] Potapov,A. and Wingender,E. (2001) Modeling the architecture of regulatory networks. In Wingender,E., Hofestaedt,R., Liebich,I. (eds.), Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig, pp. 6-10.
Category Gene Expression
Go to the abstract in the NAR 2003 Database Issue.