Leveraging transcript quantification for fast computation of alternative splicing profiles

RNA

Volumn 21, Issue 9, 2015, Pages 1521-1531

  Alamancos, Gael P ^a   Pagès, Amadís ^a,b   Trincado, Juan L ^a   Bellora, Nicolás ^c   Eyras, Eduardo ^a,d  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^c Facultad de Ciencias Naturales e Instituto M Lillo   (Argentina)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

RNA seq; Splicing; Splicing event

Indexed keywords

ACCURACY; ALTERNATIVE RNA SPLICING; ARTICLE; CYTOSOLIC FRACTION; EXON; EXON SKIPPING; HUMAN; INTRON; INTRON RETENTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA TRANSCRIPTION; ANIMAL; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS;

RNA;

ALTERNATIVE SPLICING; ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; HUMANS; RNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84939802217     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.051557.115     Document Type: Article

References (48)

1. Bechara EG, Sebestyén E, Bernardis I, Eyras E, Valcárcel J. 2013. RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation. Mol Cell 52: 720-733.
2. Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G. 2013. MITIE: simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics 29: 2529-2538.
3. Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. 2011. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res 21: 193-202.
4. David CJ, Manley JL. 2010. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev 24: 2343-2364.
5. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15-21.
6. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. 2014. Ensembl 2014. Nucleic Acids Res 42: D749-D755.
7. Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M. 2012. Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res 40: 10073-10083.
8. Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, et al. 2010. Alternative expression analysis by RNA sequencing. Nat Methods 7: 843-847.
9. Hansen KD, Brenner SE, Dudoit S. 2010. Biases in Illumina transcrip-tome sequencing caused by random hexamer priming. Nucleic Acids Res 38: e131.
10. Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, et al. 2013. DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Nucleic Acids Res 41: e39.
11. Hua Y, Liu YH, Sahashi K, Rigo F, Bennett CF, Krainer AR. 2015. Motor neuron cell-nonautonomous rescue of spinal muscular atrophy phe-notypes in mild and severe transgenic mouse models. Genes Dev 29: 288-297.
12. Katz Y, Wang ET, Airoldi EM, Burge CB. 2010. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1015.
13. Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Gervais-Bird J, Madden R, Paquet ER, Koh C, Venables JP, Prinos P, et al. 2008. Multiple alternative splicing markers for ovarian cancer. Cancer Res 68: 657-663.
14. Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, et al. 2010. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res 8: 961-974.
15. Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 323.
16. Li W, Jiang T. 2012. Transcriptome assembly and isoform expression level estimation from biased RNA-seq reads. Bioinformatics 28: 2914-2921.
17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
18. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. 2010. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26: 493-500.
19. Li W, Feng J, Jiang T. 2011a. IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. J Comput Biol 18: 1693-1707.
20. Li JJ, Jiang C-R, Brown JB, Huang H, Bickel PJ. 2011b. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc Natl Acad Sci 108: 19867-19872.
21. Maretty L, Sibbesen J, Krogh A. 2014. Bayesian transcriptome assembly. Genome Biol 15: 501.
22. Mezlini AM, Smith EJ, Fiume M, Buske O, Savich G, Shah S, Aparicion S, Chiang D, Goldenberg A, Brudno M. 2012. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res 23: 519-529.
23. Misquitta-Ali CM, Cheng E, O'Hanlon D, Liu N, McGlade CJ, Tsao MS, Blencowe BJ. 2011. Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol Cell Biol 31: 138-150.
24. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
25. Patro R, Mount SM, Kingsford C. 2014. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat Biotechnol 32: 462-464.
26. Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, et al. 2014. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 42: D756-D763.
27. Raj B, Irimia M, Braunschweig U, Sterne-Weiler T, O'Hanlon D, Lin ZY, Chen GI, Easton LE, Ule J, Gingras AC, et al. 2014. A global regulatory mechanism for activating an exon network required for neuro-genesis. Mol Cell 56: 90-103.
28. Roberts A, Pachter L. 2013. Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10: 71-73.
29. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. 2011. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12: R22.
30. Rossell D, Attolini CSO, Kroiss M, Stöcker A. 2014. Quantifying alternative splicing from paired-end RNA-sequencing data. Ann Appl Stat 8: 309-330.
31. Sebestyén E, Zawisza M, Eyras E. 2015. Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer. Nucleic Acids Res 43: 1345-1356.
32. Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y. 2012. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 40: e61.
33. Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y. 2014. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci 111: E5593-E5601.
34. Shi Y, Jiang H. 2013. rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test. PLoS One 8: e79448.
35. Simpson CG, Fuller J, Maronova M, Kalyna M, Davidson D, McNicol J, Barta A, Brown JW. 2008. Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts. Plant J 53: 1035-1048.
36. Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF. 2011. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics 27: 2633-2640.
37. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, et al. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
38. Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AM, Kruhøffer M, Laurberg S, Borre M, Wang K, et al. 2008. Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics 7: 1214-1224.
39. Tomescu AI, Kuosmanen A, Rizzi R, Mäkinen V, Veli M. 2013. A novel min-cost flow method for estimating transcript expression with RNA-Seq. BMC Bioinformatics 14: S15.
40. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 259: 1105-1111.
41. 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 iso-form switching during cell differentiation. Nat Biotechnol 28: 511-515.
42. Venables JP, Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Koh C, Gervais-Bird J, Lapointe E, Froehlich U, Durand M, et al. 2008. Identification of alternative splicing markers for breast cancer. Cancer Res 68: 9525-9531.
43. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
44. Ward A, Cooper T. 2010. The pathobiology of splicing. J. Pathol 220: 152-163.
45. Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ. 2011. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics 27: 3010-3016.
46. Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, et al. 2015. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science 347: 1254806.
47. Zhang Z, Wang W. 2014. RNA-Skim: a rapid method for RNA-Seq quantification at transcript level. Bioinformatics 30: i283-i292.
48. Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y. 2013. GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-Seq data. Genome Biol 14: R74.