Applying genetic programming to the prediction of alternative mRNA splice variants

Genomics

Volumn 89, Issue 4, 2007, Pages 471-479

  Vukusic, Ivana ^a   Grellscheid, Sushma Nagaraja ^b   Wiehe, Thomas ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Alternative splicing; Cassette exon; Feature matrix; Genetic programming; Intron retention; Splice signals

Indexed keywords

MESSENGER RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; COMPUTER PREDICTION; COMPUTER PROGRAM; EXON; GENE CASSETTE; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC PROGRAMMING; GENETIC VARIABILITY; HUMAN; INTRON; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY;

ALTERNATIVE SPLICING; BASE SEQUENCE; DATABASES, NUCLEIC ACID; EXONS; EXPERT SYSTEMS; GENOME, HUMAN; HUMANS; INTRONS; MODELS, GENETIC; SOFTWARE;

EID: 33947137243     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2007.01.001     Document Type: Article

References (41)

1. Wirth B. Spinal muscular atrophy: state-of-the-art and therapeutic perspectives. Amyotroph. Lateral Scler. Other Motor Neuron Disord. 3 (2002) 87-95
2. Kalnina Z., et al. Alterations of pre-mRNA splicing in cancer. Genes Chromosomes Cancer 42 (2005) 342-357
3. Venables J.P. Aberrant and alternative splicing in cancer. Cancer Res. 64 (2004) 7647-7654
4. Wang X.Q., et al. Alternative mRNA splicing of liver intestine-cadherin in hepatocellular carcinoma. Clin. Cancer Res. 11 2 Pt 1 (2005) 483-489
5. Zhang H., et al. Aberrant splicing of cables gene, a CDK regulator, in human cancers. Cancer Biol. Ther. 4 (2005) 1211-1215
6. Mironov A.A., Fickett J.W., and Gelfand M.S. Frequent alternative splicing of human genes. Genome Res. 9 (1999) 1288-1293
7. Brett D., et al. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett. 474 (2000) 83-86
8. Clark F., and Thanaraj T.A. Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human. Hum. Mol. Genet. 11 (2002) 451-464
9. Johnson J.M., et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302 (2003) 2141-2144
10. Stamm S., et al. ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res. 34 (2006) D46-D55 (database issue)
11. Thanaraj T.A., et al. ASD: the Alternative Splicing Database. Nucleic Acids Res. 32 (2004) D64-D69 (database issue)
12. Zheng C.L., et al. A database designed to computationally aid an experimental approach to alternative splicing. Pac. Symp. Biocomput. (2004) 78-88
13. Modrek B., and Lee C. A genomic view of alternative splicing. Nat. Genet. 30 (2002) 13-19
14. Nurtdinov R.N., et al. Low conservation of alternative splicing patterns in the human and mouse genomes. Hum. Mol. Genet. 12 (2003) 1313-1320
15. Philipps D.L., Park J.W., and Graveley B.R. A computational and experimental approach toward a priori identification of alternatively spliced exons. RNA 10 (2004) 1838-1844
16. Sorek R., et al. A non-EST-based method for exon-skipping prediction. Genome Res. 14 (2004) 1617-1623
17. Sorek R., and Ast G. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 13 (2003) 1631-1637
18. Dror G., Sorek R., and Shamir R. Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics 21 (2005) 897-901
19. Rätsch G., Sonnenburg S., and Schölkopf B. RASE: recognition of alternatively spliced exons in C. elegans. Bioinformatics 21 Suppl 1 (2005) i369-i377
20. Yeo G.W., et al. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. USA 102 (2005) 2850-2855
21. Yeo G.W. Identification, Improved Modeling and Integration of Signals to Predict Constitutive and Alternative Splicing (2004), Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge
22. Ohler U., Shomron N., and Burge C.B. Recognition of unknown conserved alternatively spliced exons. PLoS Comput. Biol. 1 (2005) e15
23. Hiller M., et al. Non-EST based prediction of exon skipping and intron retention events using Pfam information. Nucleic Acids Res. 33 (2005) 5611-5621
24. Zhang X.H., and Chasin L.A. Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev. 18 (2004) 1241-1250
25. Grellscheid S.N., and Smith C. An apparent pseudo-exon acts both as an alternative exon that leads to nonsense-mediated decay and as a zero-length exon. Mol. Cell. Biol. 26 (2006) 2237-2246
26. Gooding C., et al. A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones. Genome Biol. 7 (2006) R1
27. I. Vukusic, Vorhersage von alternativen mRNA Varianten mittels Genetischer Programmierung, Diplomarbeit, Fachbereich Informatik der Universität Dortmund: Dortmund, 2004.
28. N. Nilsson, Introduction to machine learning. Robotics Laboratory, Department of Computer Science, Stanford University, Stanford, CA: 1996.
29. Mitchell T.M. Machine learning (1997), McGraw-Hill, New York
30. Koza J.R. Genetic programming: on the programming of computers by means of natural selection (1992), MIT Press, Cambridge, MA
31. Banzhaf W., et al. Genetic programming: an introduction-on the automatic evolution of computer programs and its applications (1998), dpunkt Verlag für digitale Technologie, Heidelberg
32. Conrads M., et al. Discipulus-fast genetic programming based on AIM learning technology (2001), Register Machine Learning Technologies, Littleton, CO
33. Francone F.D., et al. Homologous crossover in genetic programming. Proceedings of the Genetic and Evolutionary Computation Conference (1999)
34. Hofacker I.L., and Stadler P.F. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22 (2006) 1172-1176
35. Kol G., Lev-Maor G., and Ast G. Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum. Mol. Genet. 14 (2005) 1559-1568
36. McCullough A.J., and Berget S.M. G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol. Cell. Biol. 17 (1997) 4562-4571
37. Zavolan M., et al. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res. 13 (2003) 1290-1300
38. Brudno M., et al. Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res. 29 (2001) 2338-2348
39. Lim L.P., and Sharp P.A. Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats. Mol. Cell. Biol. 18 (1998) 3900-3906
40. Minovitsky S., et al. The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. Nucleic Acids Res. 33 (2005) 714-724
41. Blencowe B.J. Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25 (2000) 106-110