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Related Experiment Videos

ChimerDB--a knowledgebase for fusion sequences.

Namshin Kim1, Pora Kim, Seungyoon Nam

  • 1Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea.

Nucleic Acids Research
|December 31, 2005
PubMed
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ChimerDB is a novel database cataloging gene fusions and chromosome translocations, crucial in tumor development. It aids researchers by analyzing mRNA and EST sequences for accurate fusion transcript identification.

Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Biology

Background:

  • Chromosome translocations and gene fusions are common in the human genome.
  • These events are frequently implicated as causes of various tumors.
  • Existing databases lack comprehensive fusion sequence data.

Purpose of the Study:

  • To create a comprehensive database of fusion sequences.
  • To identify and classify genuine chromosome translocations and gene fusions.
  • To provide a valuable resource for cancer research.

Main Methods:

  • Bioinformatics analysis of mRNA and expressed sequence tag (EST) sequences from GenBank.
  • Manual curation of literature data and integration with OMIM.
  • Identification of fusion transcripts with non-overlapping alignments at multiple genomic loci.

Related Experiment Videos

  • Filtering fusion events at exon-exon borders to exclude cloning artifacts.

    • Main Results:

    • ChimerDB was established, containing curated fusion sequences.
    • Identified fusion transcripts were classified into genuine translocations and intergenic splicing events.
    • Database integrates bioinformatics findings with manual literature and OMIM data.

    Conclusions:

    • ChimerDB serves as a valuable resource for studying gene fusions and translocations.
    • The database aids in assessing the validity of fusion events in cancer research.
    • Available for human, mouse, and rat genomes at http://genome.ewha.ac.kr/ChimerDB/.