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Nucleic Acids Research 2006 34(Database Issue):D21-D24; doi:10.1093/nar/gkj019
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Nucleic Acids Research, 2006, Vol. 34, Database issue D21-D24
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

ChimerDB—a knowledgebase for fusion sequences

Namshin Kim, Pora Kim, Seungyoon Nam1, Seokmin Shin2 and Sanghyuk Lee*

Division of Molecular Life Sciences, Ewha Womans University Seoul 120-750, Korea 1Interdisciplinary Program in Bioinformatics, Seoul National University Seoul 151-747, Korea 2School of Chemistry, Seoul National University Seoul 151-747, Korea

*To whom correspondence should be addressed. Tel: +82 232772888; Fax: +82 232772384; Email: sanghyuk{at}ewha.ac.kr

Received August 15, 2005. Accepted September 17, 2005.

Chromosome translocation and gene fusion are frequent events in the human genome and are often the cause of many types of tumor. ChimerDB is the database of fusion sequences encompassing bioinformatics analysis of mRNA and expressed sequence tag (EST) sequences in the GenBank, manual collection of literature data and integration with other known database such as OMIM. Our bioinformatics analysis identifies the fusion transcripts that have non-overlapping alignments at multiple genomic loci. Fusion events at exon–exon borders are selected to filter out the cloning artifacts in cDNA library preparation. The result is classified into two groups—genuine chromosome translocation and fusion between neighboring genes owing to intergenic splicing. We also integrated manually collected literature and OMIM data for chromosome translocation as an aid to assess the validity of each fusion event. The database is available at http://genome.ewha.ac.kr/ChimerDB/ for human, mouse and rat genomes.


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