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TRANSPATH: an integrated database on signal transduction and a tool for array analysis.

Mathias Krull1, Nico Voss, Claudia Choi

  • 1BIOBASE Biological Databases GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany. mkl@biobase.de

Nucleic Acids Research
|January 10, 2003
PubMed
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TRANSPATH is a comprehensive gene regulatory network database integrating signal transduction and transcription factor data. It aids in visualizing and analyzing complete signaling pathways and evaluating microarray data to identify key regulators.

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Molecular Biology

Background:

  • Gene regulatory networks (GRNs) are crucial for cellular function.
  • Signal transduction pathways and transcription factors play key roles in gene regulation.
  • Databases integrating these components are essential for comprehensive analysis.

Purpose of the Study:

  • To introduce TRANSPATH, a database system for gene regulatory networks.
  • To integrate signal transduction information with transcription factor data.
  • To provide tools for pathway visualization, analysis, and microarray data evaluation.

Main Methods:

  • Developed TRANSPATH database integrating signal transduction and TRANSFAC data.
  • Incorporated tools for pathway visualization (PathwayBuilder) and analysis.

Related Experiment Videos

  • Integrated ArrayAnalyzer for evaluating microarray data against TRANSPATH datasets.

    • Main Results:

    • TRANSPATH (release 3.2, July 2002) contains ~9800 molecules, >1800 genes, and >11,400 reactions from ~5000 references.
    • ArrayAnalyzer identifies key regulators linked to gene expression changes in microarrays.
    • PathwayBuilder offers four visualization modes for network exploration.

    Conclusions:

    • TRANSPATH provides a valuable resource for studying gene regulatory networks and signal transduction.
    • Integrated tools facilitate the analysis of complex biological pathways and gene expression data.
    • The database supports the identification of regulatory mechanisms from ligand to target genes.