title: ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.
abstract: Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/.
authors.affiliation: Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea.
authors.forename: Myunggyo
authors.identifier: 0000-0003-2015-3939
authors.initials: M
authors.lastname: Lee
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul 02841, Republic of Korea.
authors.forename: Kyubum
authors.identifier: 0000-0003-2015-3939
authors.initials: K
authors.lastname: Lee
authors.affiliation: Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea.
authors.forename: Namhee
authors.initials: N
authors.lastname: Yu
authors.affiliation: Korean Bioinformation Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
authors.forename: Insu
authors.initials: I
authors.lastname: Jang
authors.affiliation: Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 03760, Republic of Korea.
authors.forename: Ikjung
authors.initials: I
authors.lastname: Choi
authors.affiliation: Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Pora
authors.initials: P
authors.lastname: Kim
authors.affiliation: Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea.
authors.forename: Ye Eun
authors.initials: YE
authors.lastname: Jang
authors.affiliation: Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul 02841, Republic of Korea.
authors.forename: Byounggun
authors.initials: B
authors.lastname: Kim
authors.affiliation: Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul 02841, Republic of Korea.
authors.forename: Sunkyu
authors.initials: S
authors.lastname: Kim
authors.affiliation: Korean Bioinformation Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
authors.forename: Byungwook
authors.identifier: 0000-0003-2015-3939
authors.initials: B
authors.lastname: Lee
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul 02841, Republic of Korea kangj@korea.ac.kr.|Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul 02841, Republic of Korea.
authors.forename: Jaewoo
authors.initials: J
authors.lastname: Kang
authors.affiliation: Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea sanghyuk@ewha.ac.kr.|Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea.|Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 03760, Republic of Korea.
authors.forename: Sanghyuk
authors.identifier: 0000-0003-2015-3939
authors.initials: S
authors.lastname: Lee
mesh_terms: D019295:Computational Biology / Q000379:methods; D057225:Data Mining; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D012984:Software; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D015514:Oncogene Proteins, Fusion