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The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
F Schacherer1, C Choi, U Götze
1GBF German Research Centre for Biotechnology Biobase Biological Databases GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany. frs@biobase.de
Bioinformatics (Oxford, England)
|November 29, 2001
Summary
TRANSPATH is a gene-regulatory pathway information system extending TRANSFAC. It details transcription factor regulation, signaling molecules, and interactions in an object-oriented database for human, mouse, and rat.
Area of Science:
- Bioinformatics
- Molecular Biology
- Systems Biology
Background:
- TRANSPATH is an extension module of the TRANSFAC database system.
- It focuses on gene-regulatory pathways, particularly those involving transcription factors.
Purpose of the Study:
- To provide a comprehensive information system for gene-regulatory pathways.
- To store and present data on signaling molecules, complexes, and their interactions.
Main Methods:
- Utilizes an object-oriented database to store pathway elements.
- Provides interactive clickable maps and automatically generated pathway cascades.
- Data is validated with references to original publications and other databases.
Main Results:
- Stores information on gene-regulatory pathways in human, mouse, and rat.
- Includes details on signaling molecules, complexes, states, and interactions.
- Offers multiple ways to explore pathway data, including visual maps and cascades.
Conclusions:
- TRANSPATH serves as a valuable resource for studying gene-regulatory networks.
- The system integrates pathway information with cross-references to other biological databases.
- Data is available via an interactive web interface and exchangeable in XML format.