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JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Albin Sandelin1, Wynand Alkema, Pär Engström

  • 1Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, S-17177 Stockholm, Sweden.

Nucleic Acids Research
|December 19, 2003
PubMed
Summary

JASPAR provides a database of transcription factor binding site profiles for eukaryotes. These high-quality profiles, derived from experimental data, aid in analyzing genome regulatory regions.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Analysis of genome regulatory regions relies on identifying transcription factor binding sites.
  • Position-specific scoring matrices are the standard models for representing transcription factor binding specificity.

Purpose of the Study:

  • To introduce JASPAR, an open-access database of transcription factor binding site profiles.
  • To provide tools for analyzing regulatory regions in genome sequences.

Main Methods:

  • Curating annotated, high-quality, matrix-based transcription factor binding site profiles.
  • Deriving profiles exclusively from experimentally validated nucleotide sequences.
  • Developing a web interface and programming tools for analysis.

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Main Results:

  • JASPAR offers a comprehensive collection of binding site profiles for multicellular eukaryotes.
  • The database includes tools for browsing, searching, and sequence analysis.
  • Genome-wide and comparative genomic analyses are facilitated.

Conclusions:

  • JASPAR serves as a valuable resource for researchers studying gene regulation.
  • The database and associated tools enhance the analysis of transcription factor binding sites.