- ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining. [PMID: 27899563]
Myunggyo Lee, Kyubum Lee, Namhee Yu, Insu Jang, Ikjung Choi, Pora Kim, Ye Eun Jang, Byounggun Kim, Sunkyu Kim, Byungwook Lee, Jaewoo Kang, Sanghyuk Lee
Nucleic acids research 2017:45(D1)
0 Citations (Google Scholar as of 2017-02-20)
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/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
- ChimerDB 2.0--a knowledgebase for fusion genes updated. [PMID: 19906715]
Pora Kim, Suhyeon Yoon, Namshin Kim, Sanghyun Lee, Minjeong Ko, Haeseung Lee, Hyunjung Kang, Jaesang Kim, Sanghyuk Lee
Nucleic acids research 2010:38(Database issue)
55 Citations (Google Scholar as of 2017-02-20)
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.
- ChimerDB--a knowledgebase for fusion sequences. [PMID: 16381848]
Namshin Kim, Pora Kim, Seungyoon Nam, Seokmin Shin, Sanghyuk Lee
Nucleic acids research 2006:34(Database issue)
31 Citations (Google Scholar as of 2017-02-20)
Abstract: 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.