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. 2017 Jan 4;45(D1):D784-D789.
doi: 10.1093/nar/gkw1083. Epub 2016 Nov 28.

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining

Myunggyo Lee  1 , Kyubum Lee  2 , Namhee Yu  3 , Insu Jang  4 , Ikjung Choi  5 , Pora Kim  6 , Ye Eun Jang  1 , Byounggun Kim  7 , Sunkyu Kim  7 , Byungwook Lee  4 , Jaewoo Kang  8   7 , Sanghyuk Lee  9   3   5
Affiliations

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining

Myunggyo Lee et al. Nucleic Acids Res. .

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/.

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Figures

Figure 1.
Figure 1.
Overview of ChimerDB 3.0. Each number indicates the number of gene pairs from relevant resources.
Figure 2.
Figure 2.
Statistics of ChimerDB 3.0. (A) Number of gene pairs from three modules. (B) Number of gene pairs from three prediction programs.
Figure 3.
Figure 3.
User interface of ChimerDB 3.0. (A) The search window for ChimerSeq is shown as an example of supporting user query for specific data source, cancer type and prediction tools. (B) Main output is the result table showing query hits with brief summary and links to further information. A click on each row activates the fusion structure window in (C) and the detailed information window (D). Note that we support the zooming and moving capability, exon structure with domain information and the alignment of seed/junction reads if available, in the fusion structure viewer.
See this image and copyright information in PMC

References

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