Global and unbiased detection of splice junctions from RNA-seq data

被引：57

作者：

Ameur, Adam ^{[1
]}

Wetterbom, Anna ^{[1
]}

Feuk, Lars ^{[1
]}

Gyllensten, Ulf ^{[1
]}

机构：

[1] Uppsala Univ, Dept Genet & Pathol, Rudbeck Lab, SE-75185 Uppsala, Sweden

来源：

GENOME BIOLOGY | 2010年 / 11卷 / 03期

关键词：

HUMAN TRANSCRIPTOME; COMPLEXITY; CELL;

D O I：

10.1186/gb-2010-11-3-r34

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, > 31,000 splice events were predicted, of which 88% bridged between two regions separated by <= 100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions.

引用

页数：9

共 19 条

[1] Meta-analysis of indels causing human genetic disease: Mechanisms of mutagenesis and the role of local DNA sequence complexity
Chuzhanova, NA
Anassis, EJ
Ball, EV
Krawczak, M
Cooper, DN
[J]. HUMAN MUTATION, 2003, 21 (01) : 28 - 44
[2] Stem cell transcriptome profiling via massive-scale mRNA sequencing
Cloonan, Nicole
Forrest, Alistair R. R.
Kolle, Gabriel
Gardiner, Brooke B. A.
Faulkner, Geoffrey J.
Brown, Mellissa K.
Taylor, Darrin F.
Steptoe, Anita L.
Wani, Shivangi
Bethel, Graeme
Robertson, Alan J.
Perkins, Andrew C.
Bruce, Stephen J.
Lee, Clarence C.
Ranade, Swati S.
Peckham, Heather E.
Manning, Jonathan M.
McKernan, Kevin J.
Grimmond, Sean M.
[J]. NATURE METHODS, 2008, 5 (07) : 613 - 619
[3] RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
Cloonan, Nicole
Xu, Qinying
Faulkner, Geoffrey J.
Taylor, Darrin F.
Tang, Dave T. P.
Kolle, Gabriel
Grimmond, Sean M.
[J]. BIOINFORMATICS, 2009, 25 (19) : 2615 - 2616
[4] Annotating genomes with massive-scale RNA sequencing
Denoeud, France
Aury, Jean-Marc
Da Silva, Corinne
Noel, Benjamin
Rogier, Odile
Delledonne, Massimo
Morgante, Michele
Valle, Giorgio
Wincker, Patrick
Scarpelli, Claude
Jaillon, Olivier
Artiguenave, Francois
[J]. GENOME BIOLOGY, 2008, 9 (12)
[5] Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R
Domrachev, M
Lash, AE
[J]. NUCLEIC ACIDS RESEARCH, 2002, 30 (01) : 207 - 210
[6] *GNM, GNU OP SYST LIC
[7] The human genome browser at UCSC
Kent, WJ
Sugnet, CW
Furey, TS
Roskin, KM
Pringle, TH
Zahler, AM
Haussler, D
[J]. GENOME RESEARCH, 2002, 12 (06) : 996 - 1006
[8] Chimeric transcript discovery by paired-end transcriptome sequencing
Maher, Christopher A.
Palanisamy, Nallasivam
Brenner, John C.
Cao, Xuhong
Kalyana-Sundaram, Shanker
Luo, Shujun
Khrebtukova, Irina
Barrette, Terrence R.
Grasso, Catherine
Yu, Jindan
Lonigro, Robert J.
Schroth, Gary
Kumar-Sinha, Chandan
Chinnaiyan, Arul M.
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (30) : 12353 - 12358
[9] Transcriptome sequencing to detect gene fusions in cancer
Maher, Christopher A.
Kumar-Sinha, Chandan
Cao, Xuhong
Kalyana-Sundaram, Shanker
Han, Bo
Jing, Xiaojun
Sam, Lee
Barrette, Terrence
Palanisamy, Nallasivam
Chinnaiyan, Arul M.
[J]. NATURE, 2009, 458 (7234) : 97 - U9
[10] Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
Pan, Qun
Shai, Ofer
Lee, Leo J.
Frey, J.
Blencowe, Benjamin J.
[J]. NATURE GENETICS, 2008, 40 (12) : 1413 - 1415

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