A statistical method for the detection of alternative splicing using RNA-seq

PLoS ONE

Volumn 5, Issue 1, 2010, Pages

  Wang, Liguo ^a   Xi, Yuanxin ^a   Yu, Jun ^b   Dong, Liping ^a   Yen, Laising ^a   Li, Wei ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; BRAIN; EXON; HUMAN; LIVER; MMES SCORE; MOUSE; MUSCLE; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA SPLICING; SCORING SYSTEM; ALTERNATIVE RNA SPLICING; GENE EXPRESSION PROFILING; GENETICS; STATISTICAL MODEL;

ALTERNATIVE SPLICING; EXONS; GENE EXPRESSION PROFILING; LOGISTIC MODELS; MODELS, STATISTICAL; RNA, MESSENGER;

EID: 77649135463     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008529     Document Type: Article

References (19)

1. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302: 2141-2144.
2. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature.
3. 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.
4. Venables JP (2004) Aberrant and alternative splicing in cancer. Cancer Res 64: 7647-7654.
5. Grasso C, Modrek B, Xing Y, Lee C (2004) Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs. Pac Symp Biocomput. pp 29-41.
6. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 14: 331-342.
7. KapranovP,Cawley SE, DrenkowJ,Bekiranov S, StrausbergRL, et al. (2002) Largescale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
8. Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, et al. (2008) Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet.
9. Blencowe BJ, Ahmad S, Lee LJ (2009) Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23: 1379-1386.
10. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101.
11. Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res.
12. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome. Science.
13. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods.
14. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
15. Kharchenko PV, Tolstorukov MY, Park PJ (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
16. Loong TW (2003) Understanding sensitivity and specificity with the right side of the brain. BMJ 327: 716-719.
17. Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, et al. (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 34: D46-55.
18. Sharov AA, Dudekula DB, Ko MS (2005) Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res 15: 748-754.
19. Sing T, Sander O, Beerenwinkel N, Lengauer T (2005) ROCR: visualizing classifier performance in R. Bioinformatics 21: 3940-3941.