FusionCancer: a Database of Cancer Fusion Genes Derived from RNA-seq Data

Overview

Journal Diagn Pathol

Publisher Biomed Central

Specialty Pathology

Date 2015 Jul 29

PMID 26215638

Citations 45

Authors

Yunjin Wang

Nan Wu

Jiaqi Liu

Zhihong Wu

Dong Dong

Affiliations

Soon will be listed here.

Abstract

Background: Fusion genes are chimeric results originated from previous separate genes with aberrant functions. The resulting protein products may lead to abnormal status of expression levels, functions and action sites, which in return may cause the abnormal proliferation of cells and cancer development.

Results: With the emergence of next-generation sequencing technology, RNA-seq has spurred gene fusion discovery in various cancer types. In this work, we compiled 591 recently published RNA-seq datasets in 15 kinds of human cancer, and the gene fusion events were comprehensively identified. Based on the results, a database was developed for gene fusion in cancers (FusionCancer), with the attempt to provide a user-friendly utility for the cancer research community. A flexible query engine has been developed for the acquisition of annotated information of cancer fusion genes, which would help users to determine the chimera events leading to functional changes. FusionCancer can be accessible at the following hyperlink website: http://donglab.ecnu.edu.cn/databases/FusionCancer/

Conclusion: To the best of our knowledge, FusionCancer is the first comprehensive fusion gene database derived only from cancer RNA-seq data.

Citing Articles

PUM1-TRAF3 fusion protein activates non-canonical NF-κB signaling via rescued NIK in biliary tract cancer.

Jung D, Seo M, Jo J, Kim K, Kim C, Kang H NPJ Precis Oncol. 2024; 8(1):170.

PMID: 39090283 PMC: 11294552. DOI: 10.1038/s41698-024-00654-2.

Comparison of the classifiers based on mRNA, microRNA and lncRNA expression and DNA methylation profiles for the tumor origin detection.

Feng Y, Wang Y Front Genet. 2024; 15:1383852.

PMID: 38933920 PMC: 11199677. DOI: 10.3389/fgene.2024.1383852.

Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors.

Wen K, Chen X, Gu J, Chen Z, Wang Z J Biomed Sci. 2024; 31(1):63.

PMID: 38877495 PMC: 11177406. DOI: 10.1186/s12929-024-01047-0.

Clinically relevant fusion oncogenes: detection and practical implications.

Sorokin M, Rabushko E, Rozenberg J, Mohammad T, Seryakov A, Sekacheva M Ther Adv Med Oncol. 2023; 14:17588359221144108.

PMID: 36601633 PMC: 9806411. DOI: 10.1177/17588359221144108.

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.

Talsania K, Shen T, Chen X, Jaeger E, Li Z, Chen Z Genome Biol. 2022; 23(1):255.

PMID: 36514120 PMC: 9746098. DOI: 10.1186/s13059-022-02816-6.

References

. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2013; 42(Database issue):D7-17. PMC: 3965057. DOI: 10.1093/nar/gkt1146. View

Jia W, Qiu K, He M, Song P, Zhou Q, Zhou F . SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol. 2013; 14(2):R12. PMC: 4054009. DOI: 10.1186/gb-2013-14-2-r12. View

Iyer M, Chinnaiyan A, Maher C . ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011; 27(20):2903-4. PMC: 3187648. DOI: 10.1093/bioinformatics/btr467. View

Williams S, Hurst C, Knowles M . Oncogenic FGFR3 gene fusions in bladder cancer. Hum Mol Genet. 2012; 22(4):795-803. PMC: 3554204. DOI: 10.1093/hmg/dds486. View

Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W . FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics. 2011; 27(14):1922-8. DOI: 10.1093/bioinformatics/btr310. View

Robinson D, Kalyana-Sundaram S, Wu Y, Shankar S, Cao X, Ateeq B . Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat Med. 2011; 17(12):1646-51. PMC: 3233654. DOI: 10.1038/nm.2580. View

Maher C, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X . Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009; 458(7234):97-101. PMC: 2725402. DOI: 10.1038/nature07638. View

Forbes S, Bindal N, Bamford S, Cole C, Kok C, Beare D . COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2010; 39(Database issue):D945-50. PMC: 3013785. DOI: 10.1093/nar/gkq929. View

Chung G, Lung R, Hui A, Yip K, Woo J, Chow C . Identification of a recurrent transforming UBR5-ZNF423 fusion gene in EBV-associated nasopharyngeal carcinoma. J Pathol. 2013; 231(2):158-67. PMC: 4166696. DOI: 10.1002/path.4240. View

10.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S . TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):R36. PMC: 4053844. DOI: 10.1186/gb-2013-14-4-r36. View

11.

Tomlins S, Rhodes D, Perner S, Dhanasekaran S, Mehra R, Sun X . Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005; 310(5748):644-8. DOI: 10.1126/science.1117679. View

12.

Edwards P . Fusion genes and chromosome translocations in the common epithelial cancers. J Pathol. 2009; 220(2):244-54. DOI: 10.1002/path.2632. View

13.

Maher C, Palanisamy N, Brenner J, Cao X, Kalyana-Sundaram S, Luo S . Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A. 2009; 106(30):12353-8. PMC: 2708976. DOI: 10.1073/pnas.0904720106. View

14.

Kodama Y, Shumway M, Leinonen R . The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 2011; 40(Database issue):D54-6. PMC: 3245110. DOI: 10.1093/nar/gkr854. View

15.

Shyr D, Liu Q . Next generation sequencing in cancer research and clinical application. Biol Proced Online. 2013; 15(1):4. PMC: 3599179. DOI: 10.1186/1480-9222-15-4. View

16.

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

17.

Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K . Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol. 2011; 12(1):R6. PMC: 3091304. DOI: 10.1186/gb-2011-12-1-r6. View

18.

Soda M, Choi Y, Enomoto M, Takada S, Yamashita Y, Ishikawa S . Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature. 2007; 448(7153):561-6. DOI: 10.1038/nature05945. View

19.

Kim N, Kim P, Nam S, Shin S, Lee S . ChimerDB--a knowledgebase for fusion sequences. Nucleic Acids Res. 2005; 34(Database issue):D21-4. PMC: 1347382. DOI: 10.1093/nar/gkj019. View

20.

Mitelman F, Johansson B, Mertens F . The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007; 7(4):233-45. DOI: 10.1038/nrc2091. View