FUSIM: A software tool for simulating fusion transcripts

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Bruno, Andrew E ^a,b   Miecznikowski, Jeffrey C ^a,b   Qin, Maochun ^b   Wang, Jianmin ^a,b   Liu, Song ^a,b  

^a UNIVERSITY AT BUFFALO   (United States)

^b ROSWELL PARK CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHIMERIC PROTEINS; CHROMOSOMAL ABERRATION; CHROMOSOMAL REARRANGEMENT; FUSION GENES; GENE FUSION; HIGH THROUGHPUT; TRANS-SPLICING; TRANSCRIPTOMES;

BENCHMARKING; COMPUTER SOFTWARE; GENES; RNA; STATISTICAL TESTS;

ABILITY TESTING;

CHIMERIC PROTEIN; RNA;

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE FUSION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; SEQUENCE ANALYSIS;

COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE FUSION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTANT CHIMERIC PROTEINS; RNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84872180298     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-13     Document Type: Article

References (20)

1. Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 2007, 7(4):233-245.
2. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310(5748):644-648.
3. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, ichiro Fujiwara S, Watanabe H, Kurashina K, Hatanaka H, Bando M, Ohno S, Ishikawa Y, Aburatani H, Niki T, Sohara Y, Sugiyama Y, Mano H. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 2007, 448(7153):561-566.
4. Rowley JD. Chromosome translocations: dangerous liaisons revisited. Nat Rev Cancer 2001, 1(3):245-250.
5. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009, 458(7234):97-101.
6. Iyer MK, Chinnaiyan AM, Maher CA. ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics 2011, 27(20):2903-2904.
7. McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MGF, Griffith M, Moussavi AH, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol 2011, 7(5):e1001138.
8. 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):1922-1928.
9. Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JPA, Perez EA, Thompson EA. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res 2011, 39(15):e100.
10. Li Y, Chien J, Smith DI, Ma J. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics 2011, 27(12):1708-1710.
11. GenePred Table Format. [http://genome.ucsc.edu/FAQ/FAQformat.html{set minus}#format9].
12. Gene Feature Format. [http://www.sanger.ac.uk/resources/software/gff/].
13. Gene Transfer Format. [http://mblab.wustl.edu/GTF22.html].
14. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988, 85(8):2444-2448.
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. Subgroup GPDP.
16. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628.
17. Pellestor F, Anahory T, Lefort G, Puechberty J, Liehr T, Hédon B, Sarda P. Complex chromosomal rearrangements: origin and meiotic behavior. Hum Reprod Update 2011, 17(4):476-494.
18. Kim P, Yoon S, Kim N, Lee S, Ko M, Lee H, Kang H, Kim J, Lee S. ChimerDB 2.0-a knowledgebase for fusion genes updated. Nucleic Acids Res 2010, 38(Database issue):D81-D85.
19. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010, 38(6):1767-1771.
20. Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics 2012, 28(4):593-594.