Inferring global levels of alternative splicing isoforms using a generative model of microarray data

Bioinformatics

Volumn 22, Issue 5, 2006, Pages 606-613

  Shai, Ofer ^a   Morris, Quaid D ^a   Blencowe, Benjamin J ^a   Frey, Brendan J ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALTERNATIVE RNA SPLICING; ARTICLE; BAYES THEOREM; DNA HYBRIDIZATION; DNA MICROARRAY; EXON; GENE PROBE; GENE SEQUENCE; GENETIC ALGORITHM; INFORMATION PROCESSING; LEARNING; MAMMAL CELL; MICROARRAY ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROCESS DESIGN; PROCESS MONITORING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

MAMMALIA;

EID: 33644864739     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btk028     Document Type: Article

References (26)

1. Black,D.L. (2000) Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell, 103, 367-370.
2. Blanchette,M. et al. (2005) Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev., 19, 1306-1314.
3. Blencowe,B.J. (2000) Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases [Erratum (2000) Trends Biochem. Sci., 25, 228.]. Trends Biochem. Sci., 25, 106-110.
4. Cartegni,L. et al. (2002) Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rev. Gen., 3, 285-298.
5. Clark,T.A. et al. (2002) Genomewide analysis of mRNA processing in yeast using splicing specific microarrays. Science, 296, 907-910.
6. Cline,A.S. et al. (2005) ANOSVA: A statistical method for detecting splice variation from expression data. Bioinformatics, 21 (Suppl. 1), i107-i115.
7. Cozman,F. and Krotkov,E. (1995) Truncated Gaussians as tolerance sets. In Proceedings of the 5th Workshop on Artifcial Intelligence and Statistics. Springer Verlag, NY, pp. 161-167.
8. Dempster,A.P. et al. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc., B39, 1-38.
9. Durbin,B.P. and Rocke,D.M. (2004) Variance-stabilizing transformations for two-color microarrays. Bioinformatics, 20, 660-667.
10. Fehlbaum,P. et al. (2005) A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res, 33, e4.
11. Huber,W. et al. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18 (Suppl. 1), S96-S104.
12. Hui,L. et al. (2004) Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment. Oncogne, 23, 3013-3023.
13. Johnson,J.M. et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141-2144.
14. Le,K. et al. (2004) Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res., 32, e180.
15. Matlin,A.J. et al. (2005) Unterstanding alternative splicing: Towards a cellular code. Nat. Rev. Mol. Cell. Biol., 6, 386-398.
16. Maniatis,T. and Tasic,B. (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature, 418, 236-243.
17. Neal,R.M. and Hinton,G.E. (1998) A view of the EM algorithm that justifies incremental, sparse, and other variants. In Jordan,M. (ed.), Learning in Graphical Models, MIT Press, Cambridge, pp. 355-368.
18. Pan,Q. et al. (2004) Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell, 16, 929-941.
19. Pan,Q. et al. (2005) Alternative splicing of conserved exons is frequently species specific in human and mouse. Trends Genet, 21, 73-77.
20. Pearl,J. (1988) Probabilistic Reasoning in Intelligent Systems. 2nd edn. Kaufmann, San Francisco, CA.
21. Relógio,A. et al. (2005) Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. J. Biol. Chem., 280, 4779-4784.
22. Rocke,D.M. and Durbin,B. (2001) A model for measurement error for gene expression arrays. J. Compu. Biol., 8, 557-569.
23. Ule,J. et al. (2005) Nova regulates brain-specific splicing to shape the synapse. Nat. Genet., 37, 844-852.
24. Wang,H. et al. (2003a) Gene structure-based splice variant deconvolution using a microarray platform. Bioinfomatics, 19 (suppl. one), i315-i322.
25. Wang,Z. (2003b) Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer. Cancer Res., 63, 655-657.
26. Xu,Q. and Lee,C. (2003) Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res., 31, 5635-5643.