NSMAP: A method for spliced isoforms identification and quantification from RNA-Seq

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Xia, Zheng ^a,b   Wen, Jianguo ^a,b   Chang, Chung Che ^a,b   Zhou, Xiaobo ^a,b  

^a HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE SPLICING; BIOLOGICAL MECHANISMS; CURRENT REFERENCE; EXPRESSION LEVELS; MAXIMUM A POSTERIORI; MYELODYSPLASTIC SYNDROMES; NON-NEGATIVITY; TRANSCRIPTOME ANALYSIS;

ESTIMATION; GENES;

RNA;

ISOPROTEIN; MESSENGER RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; RNA SPLICING; SEQUENCE ANALYSIS;

ALTERNATIVE SPLICING; BASE SEQUENCE; GENE EXPRESSION PROFILING; HUMANS; MODELS, GENETIC; OLIGONUCLEOTIDE PROBES; PROTEIN ISOFORMS; RNA SPLICING; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 79955914959     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-162     Document Type: Article

References (36)

1. Matlin AJ, Clark F, Smith CWJ. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 2005, 6:386-398. 10.1038/nrm1645, 15956978.
2. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415. 10.1038/ng.259, 18978789.
3. Wang H, Hubbell E, shan Hu J, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D. Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics 2003, 19(Suppl 1):i315-i322. 10.1093/bioinformatics/btg1044, 12855476.
4. Caceres JF, Kornblihtt AR. Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet 2002, 18:186-193. 10.1016/S0168-9525(01)02626-9, 11932019.
5. Anton MA, Gorostiaga D, Guruceaga E, Segura V, Carmona-Saez P, Pascual-Montano A, Pio R, Montuenga LM, Rubio A. SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays. Genome Biol 2008, 9:R46. 10.1186/gb-2008-9-2-r46, 2374713, 18312629.
6. Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, et al. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 2004, 16:929-941. 10.1016/j.molcel.2004.12.004, 15610736.
7. Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM. Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol 2003, 4:R66. 10.1186/gb-2003-4-10-r66, 328455, 14519201.
8. Hiller D, Jiang H, Xu W, Wong WH. Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics 2009, 25:3056-3059. 10.1093/bioinformatics/btp544, 19762346.
9. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 2010, 26:493-500. 10.1093/bioinformatics/btp692, 2820677, 20022975.
10. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
11. Richard H, Schulz MH, Sultan M, Nurnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, et al. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucl Acids Res 2010, gkq041.
12. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
13. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:S22-S32. 10.1038/nmeth.1371, 19844228.
14. Jiang H, Wong WH. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 2009, 25:1026-1032. 10.1093/bioinformatics/btp113, 2666817, 19244387.
15. Bohnert R, Behr J, Ratsch G. Transcript quantification with RNA-Seq data. BMC Bioinformatics 2009, 10:P5.
16. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 2010, 28:511-515. 10.1038/nbt.1621, 20436464.
17. Dilworth RP. A decomposition theorem for partially ordered sets. Book A decomposition theorem for partially ordered sets 1950, 161-166. City: JSTOR, (Editor ed.^eds.). pp. 161-166..
18. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature biotechnology 2010, 28:503-510. 10.1038/nbt.1633, 2868100, 20436462.
19. Feng J, Li W, Jiang T. Inference of isoforms from short sequence reads. 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB); April 25-28, 2010; Lisbon, Portugal 2010, 138-157.
20. Aul C, Bowen DT, Yoshida Y. Pathogenesis, etiology and epidemiology of myelodysplastic syndromes. Haematologica 1998, 83:71-86.
21. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
22. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18:1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
23. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38:D613-D619.
24. Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N. Viral population estimation using pyrosequencing. PLoS Comput Biol 2008, 4:e1000074. 10.1371/journal.pcbi.1000074, 2323617, 18437230.
25. Ji S, Xue Y, Carin L. Bayesian compressive sensing. IEEE Transactions on Signal Processing 2008, 56:2346-2356.
26. Chartrand R. Exact reconstruction of sparse signals via nonconvex minimization. IEEE Signal Processing Letters 2007, 14:707-710.
27. Zhao P, Yu B. Stagewise lasso. The Journal of Machine Learning Research 2007, 8:2701-2726.
28. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
29. Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 2010,
30. Data were analyzed through the use of Ingenuity Pathways Analysis (Ingenuity® Systems, http://www.ingenuity.com).
31. Shin MG, Kajigaya S, Levin BC, Young NS. Mitochondrial DNA mutations in patients with myelodysplastic syndromes. Blood 2003, 101:3118-3125. 10.1182/blood-2002-06-1825, 12446454.
32. Lacroix V, Sammeth M, Guigo R, Bergeron A. Exact transcriptome reconstruction from short sequence reads. WABI'08: Proceedings of the 8th international workshop on Algorithms in Bioinformatics; Berlin, Heidelberg 2008, 50-63. Springer, 2703950, 19417067.
33. Salzman J, Jiang H, Wong W. Statistical modeling of rna-seq data. Book Statistical modeling of rna-seq data 2010, City: Technical Report in Biostatistics, Stanford University, (Editor ed.^eds.)..
34. Haas BJ, Zody MC. Advancing RNA-Seq analysis. Nature biotechnology 2010, 28:421-423. 10.1038/nbt0510-421, 20458303.
35. Efron B, Hastie T, Johnstone I, Tibshirani R. Least angle regression. Annals of statistics 2004, 32:407-451.
36. Casella G, Berger RL. Statistical inference 2002, Duxbury Pacific Grove, CA.