IReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data

Genome Research

Volumn 23, Issue 3, 2013, Pages 519-529

  Mezlini, Aziz M ^a,b   Smith, Eric J M ^a,b   Fiume, Marc ^a   Buske, Orion ^a   Savich, Gleb L ^c   Shah, Sohrab ^a,b,c,d   Aparicio, Sam ^b   Chiang, Derek Y ^d   Goldenberg, Anna ^a,b   Brudno, Michael ^a,b,c,e,f  

^a UNIVERSITY OF TORONTO   (Canada)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^d BRITISH COLUMBIA CANCER AGENCY   (Canada)

^e UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^f UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR; RNA ISOFORM; TRANSCRIPTOME;

ACCURACY; ALGORITHM; ALTERNATIVE RNA SPLICING; ARTICLE; CANCER CELL CULTURE; CELL STRAIN MCF 7; FALSE POSITIVE RESULT; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; HUMAN; INTRON RETENTION; NUCLEIC ACID AMPLIFICATION; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; PROBABILITY; RNA SEQUENCE; SEQUENCE ALIGNMENT; TRIPLE NEGATIVE BREAST CANCER; VALIDATION STUDY;

ALGORITHMS; COMPUTER SIMULATION; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MCF-7 CELLS; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84874597027     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.142232.112     Document Type: Article

References (30)

1. Berget S. 1995. Exon recognition in vertebrate splicing. J Biol Chem 270: 2411.
2. Bohnert R, Ratsch G. 2010. rQuant.web: A tool for RNA-seq-based transcript quantitation. Nucleic Acids Res (suppl 2) 38: W348-W351.
3. Feng J, LiW, Jiang T. 2011. Inference of isoforms from short sequence reads. J Comput Biol 18: 305-321.
4. Fiume M, Williams V, Brook A, Brudno M. 2010. Savant: Genome browser for high-throughput sequencing data. Bioinformatics 26: 1938-1944.
5. Fiume M, Smith E, Brook A, Strbenac D, Turner B, Mezlini A, Robinson M, Wodak S, Brudno M. 2012. Savant genome browser 2: Visualization and analysis for population-scale genomics. Nucleic Acids Res 40: W615-W621.
6. The FluxProject. 2011. 2011 FluxSimulator v1.0.RC4. http://flux. sammeth.net.
7. He C, Zhou F, Zuo Z, Cheng H, Zhou R. 2009. A global view of cancer-specific transcript variants by subtractive Transcriptome-Wide analysis. PLoS ONE 4: e4732.
8. Heber S, Alekseyev M, Sze S, Tang H, Pevzner PA. 2002. Splicing graphs and EST assembly problem. Bioinformatics 18: S181-S188. (Pubitemid 41185652)
9. Katz Y, Wang E, Airoldi E, Burge C. 2010. Analysis and design of rna sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1015.
10. Kim E, Goren A, Ast G. 2008. Insights into the connection between cancer and alternative splicing. Trends Genet 24: 7-10. (Pubitemid 350298628)
11. Lacroix V, Sammeth M, Guigo R, Bergeron A. 2008. Exact transcriptome reconstruction from short sequence reads. In Algorithms in bioinformatics, Vol. 5251, Lecture notes in computer science (ed. K Crandall and J Lagergren), pp. 50-63. Springer, Berlin/Heidelberg.
12. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
13. Li H, Zhang K, Jiang T. 2005. The regularized EM algorithm. In Proceedings of the 20th national conference on artificial intelligence, Vol. 2, pp. 807-812. AAAI Press, Menlo Park, C.A. (Pubitemid 43006708)
14. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. 2010. RNA-seq gene expression estimation with read mapping uncertainty. Bioinformatics 26: 493-500.
15. Li J, Jiang C, Brown J, Huang H, Bickel P. 2011. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc Natl Acad Sci 108: 19867-19872.
16. Li W, Feng J, Jiang T. 2011. IsoLasso: A LASSO regression approach to RNA-seq based transcriptome assembly. In Research in computational molecular biology, Vol. 6577, Lecture notes in computer science (ed. V Bafna and S Sahinalp), pp. 168-188. Springer, Berlin/Heidelberg.
17. Lopezbigas N, Audit B, Ouzounis C, Parra G, Guigo R. 2005. Are splicing mutations the most frequent cause of hereditary disease FEBS Lett 579: 1900-1903. (Pubitemid 40404028)
18. McLachlan G, Peel D. 2000. Finite mixture models, Vol. 299. Wiley-Interscience, Hoboken, N.J.
19. Nicolae M, Mangul S, Mandoiu I, Zelikovsky A. 2011. Estimation of alternative splicing isoform frequencies from RNA-seq data. Algorithms Mol Biol 6: 9.
20. Shah S, Roth A, Goya R, Aparicio S. 2012. The clonal and mutational evolution spectrum of primary triple negative breast cancer. Nature 7: 1009-1015.
21. Singh D, Orellana C, Hu Y, Jones C, Liu Y, Chiang D, Liu J, Prins J. 2011. Fdm: A graph-based statistical method to detect differential transcription using rna-seq data. Bioinformatics 27: 2633-2640.
22. SkotheimRI, Nees M. 2007. Alternative splicing in cancer: Noise, functional, or systematic Int J Biochem Cell Biol 39: 1432-1449.
23. Sun Z, Asmann Y, Kalari K, Bot B, Eckel-Passow J, Baker T, Carr J, Khrebtukova I, Luo S, Zhang L, et al. 2011. Integrated analysis of gene expression, cpg island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS ONE 6: e17490.
24. Tibshirani R. 1996. Regression shrinkage and selection via the lasso. J R Stat Soc Ser B Methodol 58: 267-288.
25. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25: 1105-1111.
26. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
27. Wang Z, Gerstein M, Snyder M. 2009. RNA-seq: A revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
28. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, et al. 2010. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38: e178.
29. Yoshida K, SanadaM, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, et al. 2011. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478: 64-69.
30. Zhu C, Byrd RH, Lu P, Nocedal J. 1997. Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization. ACM Trans Math Softw 23: 550-560. (Pubitemid 127447768)