ARH: Predicting splice variants from genome-wide data with modified entropy

Bioinformatics

Volumn 26, Issue 1, 2009, Pages 84-90

  Rasche, Axel ^a   Herwig, Ralf ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 75249101203     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp626     Document Type: Article

References (40)

1. Abdueva, D. et al. (2007) Experimental comparison and evaluation of the Affymetrix exon and u133plus2 genechip arrays. PLoS ONE, 2, e913.
2. Beffa, C.D. et al. (2008) Dissecting an alternative splicing analysis workflow for genechip exon 1.0 st Affymetrix arrays. BMC Genomics, 9, 571.
3. Ben-Dov, C. et al. (2008) Genome-wide analysis of alternative pre-mRNA splicing. J. Biol. Chem., 283, 1229-1233.
4. Birney, E. et al. (2006) Ensembl 2006. Nucleic Acids Res., 34, D556-D561.
5. Clark, T. et al. (2007) Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol., 8, R64.
6. Cline, M.S. et al. (2005) ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics, 21 (Suppl. 1), i107-i115.
7. Cover, T.M. and Thomas, J.A. (2006) Elements of Information Theory. 2nd edn. Hoboken, Wiley-Interscience.
8. Crooks, G.E. and Brenner, S.E. (2004) Protein secondary structure: entropy, correlations and prediction. Bioinformatics, 20, 1603-1611.
9. Dabney, A. et al. (2006) q-value: Q-value estimation for false discovery rate control. R package version 1.1.
10. Dai, M. et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res., 33, e175.
11. Das, D. et al. (2007) A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res., 35, 4845-4857.
12. Exon Array Whitepaper Collection (2005) Alternative transcript analysis methods for exon arrays. Technical Report 1.1, Affymetrix, Inc.
13. Gautier, L. et al. (2004) affy-analysis of affymetrix genechip data at the probe level. Bioinformatics, 20, 307-315.
14. Gentleman, R.C. et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
15. Gupta, S. et al. (2005) T-stag: resource and web-interface for tissue-specific transcripts and genes. Nucleic Acids Res., 33, W654-W658.
16. Herwig, R. et al. (1999) Large-scale clustering of cdna-fingerprinting data. Genome Res., 9, 1093-1105.
17. Herwig, R. et al. (2000) Information theoretical probe selection for hybridisation experiments. Bioinformatics, 16, 890-898.
18. Hu, G.K. et al. (2001) Predicting splice variant from DNAchip expression data. Genome Res., 11, 1237-1245.
19. Johnson, W.E. et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA, 103, 12457-12462.
20. Kapur, K. et al. (2007) Exon arrays provide accurate assessments of gene expression. Genome Biol., 8, R82.
21. Kasprzyk, A. et al. (2004) Ensmart: a generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
22. Koscielny, G. et al. (2009) ASTD: the alternative splicing and transcript diversity database. Genomics, 93, 213-220.
23. Margolin, A.A. et al. (2006) Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7 (Suppl. 1), S7.
24. Novoyatleva, T. et al. (2006) Pre-mRNA missplicing as a cause of human disease. In P.Jeanteur, (ed.) Alternative Splicing and Disease, vol. 44, Springer, Berlin, pp. 27- 46.
25. Pan, Q. et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
26. Purdom, E. et al. (2008) FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics, 24, 1707-1714.
27. R Development Core Team (2005) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
28. Schug, J. et al. (2005) Promoter features related to tissue specificity as measured by shannon entropy. Genome Biol., 6, R33.
29. Shah, S.H. and Pallas, J.A. (2009) Identifying differential exon splicing using linear models and correlation coefficients. BMC Bioinformatics, 10, 26.
30. Shannon, C.E. (1948) A mathematical theory of communication. Bell Syst. Technol. J., 27, 379-423.
31. Sing, T. et al. (2005) ROCR: visualizing classifier performance in R. Bioinformatics, 21, 3940-3941.
32. Srinivasan, K. et al. (2005) Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods, 37, 345-359.
33. Stamm, S. et al. (2000) An alternative-exon database and its statistical analysis. DNA Cell Biol., 19, 739-756.
34. Stamm, S. et al. (2005) Function of alternative splicing. Gene, 344, 1-20.
35. Stephenson, A.G. (2002) evd: extreme value distributions. R News, 2, 31-32.
36. Steuer, R. et al. (2002) The mutual information: detecting and evaluating dependencies between variables. Bioinformatics, 18 (Suppl. 2), S231-S240.
37. Stoilov, P. et al. (2002) Defects in pre-mRNA processing as causes of and predisposition to diseases. DNA Cell Biol., 21, 803-818.
38. Wang, E.T. et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
39. Xing, Y. et al. (2006) Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS ONE, 1, e88.
40. Xing, Y. et al. (2008) MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA, 14, 1470 1479.