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CORG: a database for COmparative Regulatory Genomics.

C Dieterich1, H Wang, K Rateitschak

  • 1Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. dieteric@molgen.mpg.de

Nucleic Acids Research
|January 10, 2003
PubMed
Summary

We identified conserved non-coding DNA sequences in human and mouse genes, likely regulatory elements. This comparative genomics approach created the CORG database for studying gene regulation.

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Area of Science:

  • Comparative Genomics
  • Regulatory Genomics
  • Bioinformatics

Background:

  • Non-coding DNA regions upstream of genes can harbor regulatory elements.
  • Sequence conservation between species suggests functional importance.
  • Identifying conserved non-coding elements aids in understanding gene regulation.

Purpose of the Study:

  • To create a comprehensive catalog of conserved non-coding sequences (CNSs) between human and mouse.
  • To develop a database, CORG (Comparative Regulatory Genomics), for accessing and visualizing these CNSs.
  • To annotate CNSs with functional information, such as EST matches and transcription factor binding sites.

Main Methods:

  • Utilized statistical local suboptimal alignments to identify conserved blocks in 15 kb upstream regions of 10,793 orthologous gene pairs.

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  • Developed the CORG database to store and manage the identified conserved non-coding blocks.
  • Annotated conserved blocks using EST matches and known transcription factor binding site data.

    • Main Results:

    • Generated a catalog of conserved non-coding sequence blocks between human and mouse.
    • Established the CORG database, accessible via web and DAS services.
    • Annotated conserved blocks to facilitate the identification of non-coding mRNA and regulatory elements.

    Conclusions:

    • Sequence conservation in upstream non-coding regions is a reliable indicator of regulatory DNA sites.
    • The CORG database provides a valuable resource for researchers studying gene regulation and comparative genomics.
    • Facilitates the discovery and analysis of functional non-coding elements across species.