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Comparative promoter region analysis powered by CORG.

Christoph Dieterich1, Steffen Grossmann, Andrea Tanzer

  • 1Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. christoph.dieterich@molgen.mpg.de

BMC Genomics
|February 23, 2005
PubMed
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We developed CORG, a framework for analyzing gene promoter regions in vertebrates. CORG integrates cross-species conservation and regulatory element predictions to aid in understanding gene regulation and discovering new elements.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Gene regulation is controlled by promoters, which dictate transcription initiation and gene expression levels.
  • Vertebrate promoter regions and transcription start sites are often poorly defined, hindering detailed analysis.
  • The CORG framework was developed to facilitate the study of upstream gene regions, including 5' untranslated exons.

Purpose of the Study:

  • To present CORG, a computational framework for the automated annotation and analysis of vertebrate promoter regions.
  • To integrate cross-species conservation data and predicted regulatory elements for enhanced promoter analysis.
  • To provide a user-friendly platform for accessing and exporting comprehensive promoter data.

Main Methods:

  • Automated annotation of promoter regions using cross-species conservation analysis (pairwise and multiple sequence comparisons).

Related Experiment Videos

  • Prediction of conserved regulatory elements via position-weight matrices and a novel approach.
  • Integration of assembled EST sequences and verified transcription start sites to distinguish exonic regions.
  • Inclusion of data from five species (human, mouse, rat, fugu, zebrafish) for 16,127 orthologous gene groups.

    • Main Results:

    • Characterization of promoter regions for over 16,000 orthologous gene groups across five vertebrate species.
    • Development of a web-based platform (CORG) for intuitive data presentation and access.
    • Demonstration of CORG's utility in phylogenetic profiling of transcription factor binding sites and microRNA detection near transcription start sites.

    Conclusions:

    • The CORG platform offers a versatile tool for analyzing gene regulation in vertebrate promoter regions.
    • CORG supports diverse applications, including the study of DNA binding site evolution and promoter composition.
    • The framework facilitates the discovery of novel regulatory sequence elements, such as microRNAs and transcription factor binding sites.