Splice Trap: A method to quantify alternative splicing under single cellular conditions

Bioinformatics

Volumn 27, Issue 21, 2011, Pages 3010-3016

  Wu, Jie ^a,b   Akerman, Martin ^a   Sun, Shuying ^a   McCombie, W Richard ^a   Krainer, Adrian R ^a   Zhang, Michael Q ^c,d  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b Stony Brook University   (United States)

^c UNIVERSITY OF TEXAS AT DALLAS   (United States)

^d TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; EVALUATION; EXON; HUMAN; SEQUENCE ANALYSIS;

ALTERNATIVE SPLICING; BAYES THEOREM; EXONS; HUMANS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 80054931745     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr508     Document Type: Article

References (27)

1. Baumer,D. et al. (2009) Alternative splicing events are a late feature of pathology in a mouse model of spinal muscular atrophy. PLoS Genet, 5, e1000773.
2. Brett,D. et al. (2002) Alternative splicing and genome complexity. Nat. Genet., 30, 29-30.
3. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
4. Castle,J.C. et al. (2008) Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat. Genet., 40, 1416-1425.
5. Clark,T.A. et al. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science, 296, 907-910.
6. Fullwood,M.J. et al. (2009) Next-generation DNAsequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res., 19, 521-532.
7. Goecks,J. et al. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
8. Gupta,S. et al. (2004) Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics, 20, 2579-2585.
9. Guttman,M. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol., 28, 503-510.
10. Jiang,H. and Wong,W.H. (2009) Statistical inferences for isoform expression in RNASeq. Bioinformatics, 25, 1026-1032.
11. Johnson,J.M., et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141-2144.
12. Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
13. Lewis,B.P. et al. (2003) Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl Acad. Sci. USA, 100, 189-192.
14. Maniatis,T. andTasic,B. (2002)Alternative pre-mRNAsplicing and proteome expansion in metazoans. Nature, 418, 236-243.
15. Pan,Q. et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
16. Peng,T. et al. (2008) Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse. BMC Genomics. 9, 191.
17. Pruitt,K.D. et al. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res., 35, D61-D65.
18. Relogio,A. et al. (2005) Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. J. Biol. Chem., 280, 4779-4784.
19. Sammeth,M. et al. (2008)Ageneral definition and nomenclature for alternative splicing events. PLoS Comput. Biol., 4, e1000147.
20. Sorek,R. et al. (2004) A non-EST-based method for exon-skipping prediction. Genome Res., 14, 1617-1623.
21. Sugnet,C.W. et al. (2004) Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac. Symp. Biocomput., 66-77.
22. Trapnell,C. et al. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
23. Trapnell,C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
24. Ule,J. et al. (2005) Nova regulates brain-specific splicing to shape the synapse. Nat. Genet., 37, 844-852.
25. Wang,E.T. et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
26. Xie,H. et al. (2002) Computational analysis of alternative splicing using EST tissue information. Genomics, 80, 326-330.
27. Zhang,C. et al. (2007) Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proc. Natl Acad. Sci. US A, 104, 15028-15033.