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Protocols

ChimerDB specifications

Information


Unique identifier OMICS_02997
Name ChimerDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 4.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ChimerDB

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Sangkyuk Lee

Publications for ChimerDB

ChimerDB citations

 (8)
library_books

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

2018
Cell Rep
PMCID: 5961503
PMID: 29617664
DOI: 10.1016/j.celrep.2018.03.076

[…] We downloaded 30,001 fusion gene (FG) transcript candidates from the ChimerSeq module of ChimerDB 3.0 (December 2016) (). By overlapping these putative fusion genes with 276 DDR genes, we identified 889 fusions involving 224 DDR genes. Among these, 464 FGs including 173 DDR genes were der […]

library_books

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

2016
Nucleic Acids Res
PMCID: 5210597
PMID: 28053160
DOI: 10.1093/nar/gkw1188

[…] in the molecular basis of disease and treatment. Cancer is covered not only by the major resource COSMIC, reporting interesting new coverage of the genetics of drug resistance, but also by updates to ChimerDB, recording chimeric transcripts, dbDEMC, containing information on miRNA expression levels in cancer, and YM500, focusing on small RNA sequences relevant to cancer. Furthermore, the update pa […]

library_books

RWCFusion: identifying phenotype specific cancer driver gene fusions based on fusion pair random walk scoring method

2016
Oncotarget
PMCID: 5308635
PMID: 27506935
DOI: 10.18632/oncotarget.11064

[…] very successful in the treatment of CML [, ]. Nowadays, several fundamental databases can provide fusion events involved in cancer. To our best knowledge, the following databases TICdb [], dbCrid [], ChimerDB 2.0 [], Mitelman [], and ChiTaRS [] contain fusion events of human cancers.The advances in next-generation sequencing (NGS) technologies help to detect gene fusions. Several tools based on ne […]

library_books

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

2016
Nucleic Acids Res
PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] ned domains of the 5′ and 3′ partners are determined, and certain domain features (e.g. oncogenic domains) are annotated. A gradient tree boosting algorithm is trained on positive driver fusions from ChimerDB 2.0 () and on a complex negative dataset (composed of passenger fusions, read-through transcripts in normal tissue, etc.). In-frame transcripts were found to by far be the most distinguishing […]

call_split

Identification of Alternative Splicing and Fusion Transcripts in Non Small Cell Lung Cancer by RNA Sequencing

2016
PMCID: 4823188
PMID: 27066085
DOI: 10.4046/trd.2016.79.2.85
call_split See protocol

[…] ncing, fusion candidate were selected. Fusion transcripts were observed only in cancer tissues, and protein coding transcripts were selected. Genes that were reported in cancer gene database (COSMIC, ChimerDB 2.0) and previous studied were validated.For Sanger sequencing, 2 µg of total RNA was used for cDNA synthesis with an oligo-dT primer and PrimeScript reverse transcription polymerase chain re […]

library_books

Transcriptome Profiling of Pediatric Core Binding Factor AML

2015
PLoS One
PMCID: 4580636
PMID: 26397705
DOI: 10.1371/journal.pone.0138782

[…] ts (2%–5%) overlapped between any two methods (). To reduce the high rate of false positives, only 69 putative fusion events (; ), identified by at least two detection methods or by one method with a ChimerDB hit[], were used in our study. ChimerDB is a knowledgebase of fusion genes identified using bioinformatics analysis of transcript sequences based on various public resources, including GenBan […]

Citations

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ChimerDB institution(s)
Department of Bio-Information Science, Ewha Womans University, Seoul, Korea; Department of Computer Science and Engineering, Korea University, Seoul, Korea; Department of Life Science, Ewha Womans University, Seoul, Korea; Korean Bioinformation Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, Korea; Ewha Research Center for Systems Biology, Ewha Womans University, Seoul, Korea; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA; Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea
ChimerDB funding source(s)
National Research Foundation of Korea (NRF-2014M3C9A3065221, NRF-2015K1A4A3047851 and NRF-2014R1A2A1A10051238), KRIBB Research Initiative Program, Technology Innovation Program of the Ministry of Trade, Industry and Energy, Republic of Korea (10050154).

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