Simultaneous Isoform Discovery and Quantification from RNA-Seq

Statistics in Biosciences

Volumn 5, Issue 1, 2013, Pages 100-118

  Hiller, David ^a   Wong, Wing Hung ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Algorithms; Alternative splicing; Isoform discovery; Monte Carlo; RNA seq

Indexed keywords

RNA ISOFORM;

ARTICLE; GENETIC DATABASE; MONTE CARLO METHOD; PARSIMONY ANALYSIS; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ANALYSIS; SIMULATION; STATISTICAL ANALYSIS;

EID: 84877035992     PISSN: 18671764     EISSN: 18671772     Source Type: Journal    
DOI: 10.1007/s12561-012-9069-2     Document Type: Article

References (40)

1. Anton MA, Gorostiaga D, Guruceaga E, Segura V, Carmona-Saez P, Pascual-Montano A, Pio R, Montuenga LM, Rubio A (2008) Space: an algorithm to predict and quantify alternatively spliced isoforms using microarrays. Genome Biol 9: R46.
2. Au KF, Jiang H, Lin L, Xing Y, Wong WH (2010) Detection of splice junctions from paired-end RNA-seq data by splicemap. Nucleic Acids Res 38(14): 4570-4578.
3. Geyer C (1991) Markov chain Monte Carlo maximum likelihood. In: Keramidas EM (ed) Computing science and statistics: Proc 23rd symposium on the interface. Interface Foundation, Fairfax Station, pp 156-163.
4. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29: 644-652.
5. Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA (2011) Comparative analysis of RNA-seq alignment algorithms and the RNA-seq unified mapper (rum). Bioinformatics 27(18): 2518-2528.
6. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincrnas. Nat Biotechnol 28: 503-510.
7. Hardcastle T, Kelly K (2010) bayseq: empirical methods for identifying differential expression in sequence count data. BMC Bioinform 11(1): 422.
8. Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA (2002) Splicing graphs and EST assembly problem. Bioinformatics 18(suppl 1): S181-S188.
9. Hiller D (2010) Alternative splicing analysis using RNA-seq data. PhD thesis, Stanford University.
10. Hiller D, Jiang H, Xu W, Wong WH (2009) Identifiability of isoform deconvolution from junction arrays and RNA-seq. Bioinformatics 25(23): 3056-3059.
11. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D (2006) The ucsc known genes. Bioinformatics 22(9): 1036-1046.
12. Hu M, Zhu Y, Taylor J, Liu J, Qin Z (2012) Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-seq. Bioinformatics 28(1): 63-68.
13. Jiang H (2009) Computational and statistical approaches in RNA sequencing analysis. PhD thesis, Stanford University.
14. Jiang H, Wong W (2009) Statistical inferences for isoform expression in RNA-seq. Bioinformatics 25(8): 1026-1032.
15. Katz Y, Wang ET, Airoldi EM, Burge CB (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1055.
16. Kim H, Bi Y, Pal S, Gupta R, Davuluri R (2011) Isoformex: isoform level gene expression estimation using weighted non-negative least squares from MRNA-seq data. BMC Bioinform 12(1): 305.
17. Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE (2007) Unproductive splicing of sr genes associated with highly conserved and ultraconserved DNA elements. Nature 446: 926-929.
18. Lee C (2003) Generating consensus sequences from partial order multiple sequence alignment graphs. Bioinformatics 19(8): 999-1008.
19. Lee S, Seo CH, Lim B, Yang JO, Oh J, Kim M, Lee S, Lee B, Kang C, Lee S (2011) Accurate quantification of transcriptome from RNA-seq data by effective length normalization. Nucleic Acids Res 39(2): e9.
20. Li B, Dewey C (2011) Rsem: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinform 12(1): 323.
21. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP (2009) The sequence alignment/map format and samtools. Bioinformatics 25(16): 2078-2079.
22. 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(50): 19, 867-19, 872.
23. Li J, Jiang H, Wong W (2010) Modeling non-uniformity in short-read rates in RNA-seq data. Genome Biol 11(5): R50.
24. Li W, Feng J, Jiang T (2011) Isolasso: a lasso regression approach to RNA-seq based transcriptome assembly. J Comput Biol 18(11): 1693-1707.
25. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12(10): 671-682.
26. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5(7): 621-628.
27. 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.
28. 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. doi: 10. 1186/gb-2011-12-3-r22.
29. Robinson MD, McCarthy DJ, Smyth GK (2010) edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1): 139-140.
30. Salzman J, Jiang H, Wong W (2011) Statistical modeling of RNA-seq data. Stat Sci 26(1): 62-83.
31. Shen S, Won Park J, Huang J, Dittmar K, Lu Z, Zhou Q, Carstens R, Xing Y (2012) Mats: a Bayesian framework for flexible detection of differential alternative splicing from RNA-seq data. Nucleic Acids Res 40(8): e61.
32. Stegle O, Drewe P, Bohnert R, Borgwardt K, Rätsch G (2010) Statistical tests for detecting differential RNA-transcript expression from read counts. Available on nature precedings. http://precedings. nature. com/documents/4437/version/1.
33. Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A (2011) Differential expression in RNA-seq: a matter of depth. Genome Res. doi: 10. 1101/gr. 124321. 111. URL http://genome. cshlp. org/content/early/2011/10/28/gr. 124321. 111. abstract.
34. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25(9): 1105-1111.
35. Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg S, Wold B, Pachter L (2010) Transcript assembly and abundance estimation from RNA-seq reveals thousands of new transcripts and switching among isoforms. Nat Biotechnol 28: 511-515.
36. 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.
37. Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D (2003) Gene structure-based splice variant deconvolution using a microarry platform. Bioinformatics 19: i315-i322.
38. Xia Z, Wen J, Chang CC, Zhou X (2011) Nsmap: a method for spliced isoforms identification and quantification from RNA-seq. BMC Bioinform 12(1): 162. doi: 10. 1186/1471-2105-12-162. URL http://www. biomedcentral. com/1471-2105/12/162.
39. Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C (2006) An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 34(10): 3150-3160.
40. Zhou YH, Xia K, Wright FA (2011) A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics 27(19): 2672-2678.