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Related Experiment Videos

ARED 3.0: the large and diverse AU-rich transcriptome.

Tala Bakheet1, Bryan R G Williams, Khalid S A Khabar

  • 1Department of Biostatistics, Epidemiology, and Scientific Computing (Bioinformatics Section), King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.

Nucleic Acids Research
|December 31, 2005
PubMed
Summary

The updated AU-rich elements (AREs) database (ARED) now includes 4000 ARE-mRNAs, representing 5-8% of human genes. This database enhances understanding of mRNA regulation in health and disease.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • AU-rich elements (AREs) are critical RNA regulatory motifs found in messenger RNAs (mRNAs).
  • Understanding AREs is vital for comprehending mRNA turnover, gene expression regulation, and their roles in various biological processes and diseases.
  • Previous databases may have lacked comprehensive data or advanced search functionalities for ARE-containing mRNAs.

Purpose of the Study:

  • To present a significantly updated and enhanced version of the AU-rich elements containing mRNA database (ARED).
  • To improve accessibility and analytical capabilities for researchers studying ARE-mRNAs.
  • To provide a more comprehensive resource for investigating the role of AREs in human biology and disease.

Main Methods:

  • Conducted a comprehensive search using extensive mRNA data from human genome databases and the expressed sequence tag (EST) database.

Related Experiment Videos

  • Collected and curated a large set of ARE-mRNAs, including alternative forms.
  • Developed an enhanced website with new functionalities for data retrieval and analysis, integrating with NCBI resources.

    • Main Results:

    • Recovered approximately 4000 ARE-mRNAs, constituting 5-8% of human genes.
    • The updated ARED website offers enhanced search capabilities, including ARE classification, clustering, source mRNA details, EST evidence, and integration with Entrez ID and Unigene.
    • Gene Ontology analysis revealed significant functional diversity among ARE-genes, particularly in regulatory processes, response to stimuli, RNA metabolism, and developmental processes.

    Conclusions:

    • The updated ARED is a larger, more diverse, and functionally enhanced resource for studying ARE-mRNAs.
    • ARE-genes play significant roles in crucial cellular functions, including regulation, response to stimuli, and development.
    • This comprehensive database facilitates research into mRNA turnover and the implications of AREs in health and disease.