ChimerDB 3.0

An enhanced database for fusion genes from cancer transcriptome and literature data mining

Myunggyo Lee, Kyubum Lee, Namhee Yu, Insu Jang, Ikjung Choi, Pora Kim, Ye EunJang, Byounggun Kim, Sunkyu Kim, Byungwook Lee, Jaewoo Kang, Sanghyuk Lee

Research output: Contribution to journalArticle

22 Citations (Scopus)

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/.

Original languageEnglish
Pages (from-to)D784-D789
JournalNucleic Acids Research
Volume45
Issue numberD1
DOIs
Publication statusPublished - 2017 Jan 1

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Data Mining
Neoplasm Genes
Gene Fusion
Transcriptome
Data mining
Fusion reactions
Genes
Databases
High-Throughput Nucleotide Sequencing
Atlases
PubMed
Neoplasms
Genome
RNA
Knowledge Bases
User interfaces

ASJC Scopus subject areas

  • Genetics

Cite this

ChimerDB 3.0 : An enhanced database for fusion genes from cancer transcriptome and literature data mining. / Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; EunJang, Ye; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk.

In: Nucleic Acids Research, Vol. 45, No. D1, 01.01.2017, p. D784-D789.

Research output: Contribution to journalArticle

Lee, M, Lee, K, Yu, N, Jang, I, Choi, I, Kim, P, EunJang, Y, Kim, B, Kim, S, Lee, B, Kang, J & Lee, S 2017, 'ChimerDB 3.0: An enhanced database for fusion genes from cancer transcriptome and literature data mining', Nucleic Acids Research, vol. 45, no. D1, pp. D784-D789. https://doi.org/10.1093/nar/gkw1083
Lee, Myunggyo ; Lee, Kyubum ; Yu, Namhee ; Jang, Insu ; Choi, Ikjung ; Kim, Pora ; EunJang, Ye ; Kim, Byounggun ; Kim, Sunkyu ; Lee, Byungwook ; Kang, Jaewoo ; Lee, Sanghyuk. / ChimerDB 3.0 : An enhanced database for fusion genes from cancer transcriptome and literature data mining. In: Nucleic Acids Research. 2017 ; Vol. 45, No. D1. pp. D784-D789.
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