title: ChimerDB 2.0--a knowledgebase for fusion genes updated.
abstract: 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.
authors.affiliation: Division of Life and Pharmaceutical Sciences, Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Korea.
authors.forename: Pora
authors.initials: P
authors.lastname: Kim
authors.forename: Suhyeon
authors.initials: S
authors.lastname: Yoon
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.forename: Sanghyun
authors.initials: S
authors.lastname: Lee
authors.forename: Minjeong
authors.initials: M
authors.lastname: Ko
authors.forename: Haeseung
authors.initials: H
authors.lastname: Lee
authors.forename: Hyunjung
authors.initials: H
authors.lastname: Kang
authors.forename: Jaesang
authors.initials: J
authors.lastname: Kim
authors.forename: Sanghyuk
authors.initials: S
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D000818:Animals; D002875:Chromosomes; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020869:Gene Expression Profiling; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D039781:PubMed; D012984:Software; D014178:Translocation, Genetic