Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs

Bioinformatics

Volumn 29, Issue 18, 2013, Pages 2300-2310

  Legault, Laura H ^a   Dewey, Colin N ^a,b  

^a University of Wisconsin   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALTERNATIVE RNA SPLICING; ANIMAL; ARTICLE; CELL LINE; COMPUTER PROGRAM; DROSOPHILA; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS; STATISTICAL MODEL; PROCEDURES;

ALGORITHMS; ALTERNATIVE SPLICING; ANIMALS; CELL LINE; DROSOPHILA; GENE EXPRESSION PROFILING; HUMANS; MODELS, STATISTICAL; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84883469280     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt396     Document Type: Article

References (44)

1. Bohnert,R. et al. (2009) Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10 (Suppl. 13), P5.
2. Bollina,D. et al. (2006) ASGS: An alternative splicing graph web service. Nucleic Acids Res., 34, W444-W447.
3. Chang,H. et al. (2005) The application of alternative splicing graphs in quantitative analysis of alternative splicing form from EST database. Int. J. Comput. Appl. Technol., 22, 14-22.
4. Cherbas,L. et al. (2011) The transcriptional diversity of 25 Drosophila cell lines. Genome Res., 21, 301-314.
5. Dye,M.J. et al. (2006) Exon tethering in transcription by RNA polymerase II. Mol. Cell, 21, 849-859.
6. Emerick,M.C. et al. (2006) Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: Alternative structures, developmental expression, and biophysical variations. Proteins, 64, 320-342.
7. Fededa,J.P. et al. (2005) A polar mechanism coordinates different regions of alternative splicing within a single gene. Mol. Cell, 19, 393-404.
8. Grabherr,M.G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652.
9. Graveley,B.R. et al. (2011) The developmental transcriptome of Drosophila melanogaster. Nature, 471, 473-479.
10. 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.
11. Hansen,K.D. et al. (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res., 38, e131.
12. Hansen,K.D. et al. (2011) Sequencing technology does not eliminate biological variability. Nat. Biotechnol., 29, 572-573.
13. Heber,S. et al. (2002) Splicing graphs and EST assembly problem. Bioinformatics, 18 (Suppl. 1), S181-S188.
14. Hiller,D. et al. (2009) Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics, 25, 3056-3059.
15. Hsu,F. et al. (2006) The UCSC known genes. Bioinformatics, 22, 1036-1046.
16. Jenkins,P. et al. (2006) How many transcripts does it take to reconstruct the Splice Graph?. Algorithms Bioinform., 4175, 103-114.
17. Jiang,H. and Wong,W.H. (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics, 25, 1026-1032.
18. Kakaradov,B. et al. (2012) Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. BMC Bioinformatics, 13 (Suppl. 6), S11.
19. Katz,Y. et al. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods, 7, 1009-1015.
20. Lacroix,V. et al. (2008) Exact transcriptome reconstruction from short sequence reads. Algorithms Bioinform., 5251, 50-63.
21. Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
22. Li,B. et al. (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26, 493-500.
23. Li,J. et al. (2010) Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol., 11, R50.
24. Li,J.J. et al. (2011) Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc. Natl Acad. Sci. USA, 108, 19867-19872.
25. Li,W. et al. (2011) IsoLasso: A LASSO regression approach to RNA-Seq based transcriptome assembly. In: Research in Computational Molecular Biology. Springer, Berlin Heidelberg, pp. 168-188.
26. Matlin,A.J. et al. (2005) Understanding alternative splicing: Towards a cellular code. Nat. Rev. Mol. Cell Biol., 6, 386-398.
27. Montgomery,S.B. et al. (2010) Transcriptome genetics using second generation sequencing in a caucasian population. Nature, 464, 773-777.
28. Neves,G. et al. (2004) Stochastic yet biased expression of multiple Dscam splice variants by individual cells. Nat. Genet., 36, 240-246.
29. Nicolae,M. et al. (2010) Estimation of alternative splicing isoform frequencies from RNA-Seq data. In: Moulton,V. and Singh,M. (eds) Algorithms in Bioinformatics, Lecture Notes in Computer Science. Vol. 6293, Springer Berlin, Heidelberg, pp. 202-214.
30. Richard,H. et al. (2010) Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res., 38, e112.
31. Roberts,A. et al. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol., 12, R22.
32. Robertson,G. et al. (2010) De novo assembly and analysis of RNA-seq data. Nat. Methods, 7, 909-912.
33. Rogers,M.F. et al. (2012) SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biol., 13, R4.
34. Schmucker,D. et al. (2000) Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell, 101, 671-684.
35. Singh,D. et al. (2011) FDM: A graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics, 27, 2633-2640.
36. Smith,C.D. et al. (2007) The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science, 316, 1586-1591.
37. The ENCODE Project Consortium. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
38. Trapnell,C. et al. (2009) TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
39. 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.
40. Trapnell,C. et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol., 31, 46-53.
41. Wang,E.T. et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
42. Wang,Z. et al. (2009) RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
43. Xia,Z. et al. (2011) NSMAP: A method for spliced isoforms identification and quantification from RNA-Seq. BMC Bioinform., 12, 162.
44. Xing,Y. et al. (2006) An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res., 34, 3150-3160.