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TRANSFAC: an integrated system for gene expression regulation.

E Wingender1, X Chen, R Hehl

  • 1Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig, Germany. ewi@gbf.de

Nucleic Acids Research
|December 11, 1999
PubMed
Summary

The TRANSFAC database now includes enhanced information on transcription factors, their binding sites, and DNA profiles. New modules offer data on disease-related mutations and DNA regions, improving its utility for researchers.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • TRANSFAC is a key database for transcription factors, genomic binding sites, and DNA-binding profiles.
  • Existing content is being expanded with new data types and functionalities.

Purpose of the Study:

  • To enhance the TRANSFAC database with new information and modules.
  • To improve the discoverability and utility of transcription factor and related genomic data.

Main Methods:

  • Expansion of existing TRANSFAC content with training sequences and plant-specific data.
  • Integration of new modules: PathoDB for pathological mutations and S/MARt DB for DNA-binding proteins.
  • Extension and integration of TRANSPATH (signal transduction) and CYTOMER (cell types) databases.

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Main Results:

  • TRANSFAC now includes detailed information on training sequences for nucleotide matrices.
  • New modules provide data on plant transcription factors and binding sites.
  • PathoDB offers insights into mutations affecting regulatory regions and transcription factor genes.
  • S/MARt DB details scaffold/matrix attached regions and their associated proteins.
  • Enhanced integration with signal transduction and cell type databases.

Conclusions:

  • The enhanced TRANSFAC database offers a more comprehensive resource for studying transcription factors and gene regulation.
  • New modules and integrated databases increase the scope and applicability of TRANSFAC for various research areas.
  • These updates facilitate deeper understanding of gene regulation, disease mechanisms, and genomic organization.