Warning: The NCBI web site requires JavaScript to function. more...

My NCBI Sign In

Result Filters

Genome Biol. 2011 Aug 11;12(8):R72.

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Kim D, Salzberg SL.

Source

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. infphilo@umiacs.umd.edu

Abstract

TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/.

PMID:: 21835007; [PubMed - indexed for MEDLINE]
PMCID:: PMC3245612

Free PMC Article

Images from this publication.See all images (6) Free text

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Libraries

LinkOut Holdings

Supplemental Content

Icon for BioMed Central

Icon for PubMed Central

Save items

loading

Related citations in PubMed

TopHat: discovering splice junctions with RNA-Seq. [Bioinformatics. 2009]
TopHat: discovering splice junctions with RNA-Seq.
Trapnell C, Pachter L, Salzberg SL. Bioinformatics. 2009 May 1; 25(9):1105-11. Epub 2009 Mar 16.
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. [BMC Med Genomics. 2011]
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines.
Ha KC, Lalonde E, Li L, Cavallone L, Natrajan R, Lambros MB, Mitsopoulos C, Hakas J, Kozarewa I, Fenwick K, et al. BMC Med Genomics. 2011 Oct 27; 4:75. Epub 2011 Oct 27.
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. [PLoS Comput Biol. 2011]
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, et al. PLoS Comput Biol. 2011 May; 7(5):e1001138. Epub 2011 May 19.
Review A comparison of analog and Next-Generation transcriptomic tools for mammalian studies. [Brief Funct Genomics. 2011]
Review A comparison of analog and Next-Generation transcriptomic tools for mammalian studies.
Roy NC, Altermann E, Park ZA, McNabb WC. Brief Funct Genomics. 2011 May; 10(3):135-50. Epub 2011 Mar 9.
Review Sequencing transcriptomes in toto. [Integr Biol (Camb). 2011]
Review Sequencing transcriptomes in toto.
Kassahn KS, Waddell N, Grimmond SM. Integr Biol (Camb). 2011 May; 3(5):522-8. Epub 2011 Feb 4.

See reviews... See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC

Recent activity

Clear Turn Off Turn On

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Genome Biol. 2011 Aug 11 ;12(8):R72.

PubMed
The mature-parasite-infected erythrocyte surface antigen (MESA) of Plasmodium fa...
The mature-parasite-infected erythrocyte surface antigen (MESA) of Plasmodium falciparum associates with the erythrocyte membrane skeletal protein, band 4.1.
Mol Biochem Parasitol. 1990 Jan 15 ;38(2):261-70.

PubMed
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gen...
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.
Genome Biol. 2011 Jul 28 ;12(7):R69.

PubMed
Consensus patterns in DNA.
Consensus patterns in DNA.
Methods Enzymol. 1990 ;183:211-21.

PubMed
The minimal kinome of Giardia lamblia illuminates early kinase evolution and uni...
The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology.
Genome Biol. 2011 Jul 25 ;12(7):R66.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

You are here: NCBI > Literature > PubMed

Write to the Help Desk