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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp982
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

ChimerDB 2.0—a knowledgebase for fusion genes updated

Pora Kim1,2, Suhyeon Yoon1,2, Namshin Kim3, Sanghyun Lee2, Minjeong Ko1,2, Haeseung Lee1,2, Hyunjung Kang1,2, Jaesang Kim1,2 and Sanghyuk Lee1,2,*

1Division of Life and Pharmaceutical Sciences, 2Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750 and 3Bioinformatics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea

*To whom correspondence should be addressed. Tel: +82 2 3277 2888; Fax: +82 2 3277 3760; Email: sanghyuk{at}ewha.ac.kr

Received September 8, 2009. Revised October 15, 2009. Accepted October 15, 2009.

Chromosome translocations and gene fusions are frequent events in the human genome and have been found to cause diverse types of tumor. ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman’s database. In this updated version, we significantly modified the algorithm of identifying fusion transcripts. Specifically, the new algorithm is more sensitive and has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Importantly, results from the analysis of next-generation sequencing data in the short read archives are incorporated as well. We updated and integrated all contents (GenBank, Sanger CGP, OMIM, PubMed publications and the Mitelman’s database), and the user-interface has been improved to support diverse types of searches and to enhance the user convenience especially in browsing PubMed articles. We also developed a new alignment viewer that should facilitate examining reliability of fusion transcripts and inferring functional significance. We expect ChimerDB 2.0, available at http://ercsb.ewha.ac.kr/fusiongene, to be a valuable tool in identifying biomarkers and drug targets.

The authors wish it to be known that, in their opinion, the first four authors should be regarded as joint First Authors.


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