Abstract
TRANSPATH is a database system about gene regulatory networks that combines encyclopedic information on signal transduction with tools for visualization and analysis. The integration with TRANSFAC, a database about transcription factors and their DNA binding sites, provides the possibility to obtain complete signaling 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 >11 400 reactions collected from approximately 5000 references. With the ArrayAnalyzer, 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, a tool that offers four different modes of visualization. More information on TRANSPATH is available at http://www.biobase.de/pages/products/databases.html.
Highlights
The mammalian genome is regulated by a plethora of transcription factors
Their activity depends on signals that are transmitted by extra- and intracellular pathways
Today, signaling specificity is not entirely understood and, among other things, can result from specific spatiotemporal distribution of signaling molecules, well directed degradation, modulation of kinetics, nongeneric receptors or tissue-specific effectors [1,2]. Knowledge about these mechanisms is essential for understanding cellular behavior and predicting the causes of dysregulation, which can lead to cancer or other diseases
Summary
Published in Krull, M., Voss, N., Choi, C., Pistor, S., Potapov, A., Wingender, E. TRANSPATH®: An integrated database on signal transduction and a tool for array analysis (2003) Nucleic Acids Research, 31 [1], pp. TRANSPATH1: an integrated database on signal transduction and a tool for array analysis. Mathias Krull1,*, Nico Voss, Claudia Choi, Susanne Pistor, Anatolij Potapov and Edgar Wingender
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