메뉴 건너뛰기




Volumn 4, Issue 4, 2010, Pages 411-430

Prediction of alternatively spliced exons using support vector machines

Author keywords

Bioinformatics; Feature construction; Pre mRNA alternative splicing; Splicing motifs; Support vector machines; SVMs

Indexed keywords

ISOPROTEIN;

EID: 77954700410     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2010.034197     Document Type: Article
Times cited : (16)

References (39)
  • 1
    • 5044222204 scopus 로고    scopus 로고
    • How did alternative splicing evolve?
    • Ast, G. (2004) 'How did alternative splicing evolve?', Nat. Rev. Genet., Vol. 5, No. 10, pp. 773-782.
    • (2004) Nat. Rev. Genet. , vol.5 , Issue.10 , pp. 773-782
    • Ast, G.1
  • 3
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: Application to sequence homology searches
    • Bailey, T. and Gribskov, M. (1998) 'Combining evidence using p-values: application to sequence homology searches', Bioinformatics, Vol. 14, No. 1, pp. 48-54.
    • (1998) Bioinformatics , vol.14 , Issue.1 , pp. 48-54
    • Bailey, T.1    Gribskov, M.2
  • 4
    • 4944225083 scopus 로고    scopus 로고
    • Remote homology detection: A motif based approach
    • Ben-Hur, A. and Brutlag, D. (2003) 'Remote homology detection: a motif based approach', Bioinformatics, Vol. 19, Suppl. 1, pp. 23-26.
    • (2003) Bioinformatics , vol.19 , Issue.1 SUPPL. , pp. 23-26
    • Ben-Hur, A.1    Brutlag, D.2
  • 5
    • 33747823564 scopus 로고    scopus 로고
    • MEME: Discovering and analyzing DNA and protein sequence motifs
    • Bailey, T., Williams, N., Misleh, C. and Li, W. (2006) 'MEME: discovering and analyzing DNA and protein sequence motifs', Nucleic Acids Research, Vol. 34, pp. 369-373.
    • (2006) Nucleic Acids Research , vol.34 , pp. 369-373
    • Bailey, T.1    Williams, N.2    Misleh, C.3    Li, W.4
  • 6
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: Exonic mutations that affect splicing
    • Cartegni, L., Chew, S. and Krainer, A. (2002) 'Listening to silence and understanding nonsense: exonic mutations that affect splicing', Nature Reviews Genetics, Vol. 3, No. 4, pp. 285-298.
    • (2002) Nature Reviews Genetics , vol.3 , Issue.4 , pp. 285-298
    • Cartegni, L.1    Chew, S.2    Krainer, A.3
  • 7
    • 16344396421 scopus 로고    scopus 로고
    • Accurate identification of alternatively spliced exons using support vector machine
    • Dror, G., Sorek, R. and Shamir, R. (2005) 'Accurate identification of alternatively spliced exons using support vector machine', Bioinformatics, Vol. 21, No. 7, pp. 897-901.
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 897-901
    • Dror, G.1    Sorek, R.2    Shamir, R.3
  • 8
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancer motifs in human protein-coding genes
    • Fairbrother, W., Yeh, R. F., Sharp, P. and Burge, C. (2002) 'Predictive identification of exonic splicing enhancer motifs in human protein-coding genes', Science, Washington DC, USA, Vol. 297, No. 5583, pp. 1007-1013.
    • (2002) Science, Washington DC, USA , vol.297 , Issue.5583 , pp. 1007-1013
    • Fairbrother, W.1    Yeh, R.F.2    Sharp, P.3    Burge, C.4
  • 9
    • 35248901812 scopus 로고    scopus 로고
    • Gene expression, intron density and splice site strength in drosophila and caenorhabditis
    • Fahey, E. and Higgins, D. G. (2007) 'Gene expression, intron density and splice site strength in drosophila and caenorhabditis', Journal of Molecular Evolution, Vol. 65, No. 3, pp. 349-357.
    • (2007) Journal of Molecular Evolution , vol.65 , Issue.3 , pp. 349-357
    • Fahey, E.1    Higgins, D.G.2
  • 10
    • 0018263844 scopus 로고
    • Why genes in pieces?
    • Gilbert, W. (1978) 'Why genes in pieces?', Nature, Vol. 271, No. 5645, p. 50.
    • (1978) Nature , vol.271 , Issue.5645 , pp. 50
    • Gilbert, W.1
  • 11
    • 0035252410 scopus 로고    scopus 로고
    • Alternative splicing: Increasing diversity in the proteomic world
    • Graveley, B. (2001) 'Alternative splicing: increasing diversity in the proteomic world', Trends Genet., Vol. 17, No. 2, pp. 100-107.
    • (2001) Trends Genet. , vol.17 , Issue.2 , pp. 100-107
    • Graveley, B.1
  • 12
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon, I., Weston, J., Barnhill, S. and Vapnik, V. (2002) 'Gene selection for cancer classification using support vector machines', Machine Learning, Vol. 46, pp. 389-422.
    • (2002) Machine Learning , vol.46 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnik, V.4
  • 13
    • 37349056702 scopus 로고    scopus 로고
    • Pre-mRNA secondary structures influence exon recognition
    • Hiller, M., Zhang, Z. Y., Backofen, R. and Stamm, S. (2007) 'Pre-mRNA secondary structures influence exon recognition', PLoS Comput. Biol., Vol. 3, No. 11, p. 204.
    • (2007) PLoS Comput. Biol. , vol.3 , Issue.11 , pp. 204
    • Hiller, M.1    Zhang, Z.Y.2    Backofen, R.3    Stamm, S.4
  • 14
    • 38949107416 scopus 로고    scopus 로고
    • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events
    • Holste, D. and Ohle, U. (2008) 'Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events', PLoS Comput. Biol., Vol. 4, No. 1, p. 21.
    • (2008) PLoS Comput. Biol. , vol.4 , Issue.1 , pp. 21
    • Holste, D.1    Ohle, U.2
  • 17
    • 0035036534 scopus 로고    scopus 로고
    • Gene structure prediction and alternative splicing analysis using genomically aligned EST
    • Kan, Z. Y., Rouchka, E. C., Gish, W. R. and States, D. J. (2001) 'Gene structure prediction and alternative splicing analysis using genomically aligned EST', Genome Res., Vol. 11, No. 5, pp. 889-900.
    • (2001) Genome Res. , vol.11 , Issue.5 , pp. 889-900
    • Kan, Z.Y.1    Rouchka, E.C.2    Gish, W.R.3    States, D.J.4
  • 18
    • 33746609827 scopus 로고    scopus 로고
    • Intronic alternative splicing regulators identified by comparative genomics in nematodes
    • Kabat, J. L., Barberan-Soler, S., McKenna, P., Clawson, H., Farrer, T. and Zahler, A. M. (2006) 'Intronic alternative splicing regulators identified by comparative genomics in nematodes', PLoS Comput. Biol., Vol. 2, No. 7, p. 86.
    • (2006) PLoS Comput. Biol. , vol.2 , Issue.7 , pp. 86
    • Kabat, J.L.1    Barberan-Soler, S.2    McKenna, P.3    Clawson, H.4    Farrer, T.5    Zahler, A.M.6
  • 19
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • The International Genome Sequencing Consortium
    • Lander, E. S., Linton, L. M. et al. (2001) 'Initial sequencing and analysis of the human genome', Nature, The International Genome Sequencing Consortium, Vol. 409, No. 6822, pp. 860-921.
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2
  • 20
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • Leslie, C., Eskin, E., Cohen, A., Weston, J. and Noble, W. (2003) 'Mismatch string kernels for discriminative protein classification', Bioinformatics, Vol. 20, No. 4, pp. 467-476.
    • (2003) Bioinformatics , vol.20 , Issue.4 , pp. 467-476
    • Leslie, C.1    Eskin, E.2    Cohen, A.3    Weston, J.4    Noble, W.5
  • 21
    • 0001673996 scopus 로고    scopus 로고
    • A comparison of event models for naive bayes text classification
    • Tech. Rep. WS-98-05, Madison, Wisconsin
    • McCallum, A. and Nigam, K. (1998) 'A comparison of event models for naive bayes text classification', AAAI-98 Workshop on Learning for Text Categorization, Tech. Rep. WS-98-05, Madison, Wisconsin.
    • (1998) AAAI-98 Workshop on Learning for Text Categorization
    • McCallum, A.1    Nigam, K.2
  • 22
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D., Sabina, J., Zuker, M. and Turner, D. (1999) 'Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure', Journal of Molecular Biology, Vol. 288, No. 5, pp. 911-940.
    • (1999) Journal of Molecular Biology , vol.288 , Issue.5 , pp. 911-940
    • Mathews, D.1    Sabina, J.2    Zuker, M.3    Turner, D.4
  • 24
    • 33846474760 scopus 로고    scopus 로고
    • A hitchhiker's guide to expressed sequence tag (EST) analysis
    • Nagaraj, S. H., Gasser, R. B. and Ranganathan, S. (2006) 'A hitchhiker's guide to expressed sequence tag (EST) analysis', Brief Bioinform., Vol. 8, No. 1, pp. 6-21.
    • (2006) Brief Bioinform. , vol.8 , Issue.1 , pp. 6-21
    • Nagaraj, S.H.1    Gasser, R.B.2    Ranganathan, S.3
  • 26
    • 34249987613 scopus 로고    scopus 로고
    • A computational survey of candidate exonic splicing enhancer motifs in the model plant arabidopsis thaliana
    • Pertea, M., Mount, S. M. and Salzberg, S. L. (2007) 'A computational survey of candidate exonic splicing enhancer motifs in the model plant arabidopsis thaliana', BMC Bioinformatics, Vol. 8, p. 159.
    • (2007) BMC Bioinformatics , vol.8 , pp. 159
    • Pertea, M.1    Mount, S.M.2    Salzberg, S.L.3
  • 27
    • 29144512262 scopus 로고    scopus 로고
    • RASE: Recognition of alternatively spliced exons in C. elegans
    • Rätsch, G., Sonnenburg, S. and Schölkof, B. (2005) 'RASE: recognition of alternatively spliced exons in C. elegans', Bioinformatics, Vol. 21, Suppl. 1, pp. 369-377.
    • (2005) Bioinformatics , vol.21 , Issue.1 SUPPL. , pp. 369-377
    • Rätsch, G.1    Sonnenburg, S.2    Schölkof, B.3
  • 29
    • 0038486897 scopus 로고    scopus 로고
    • Intronic sequences flanking alternatively spliced exons are conserved between human and mouse
    • Sorek, R. and Ast, G. (2003) 'Intronic sequences flanking alternatively spliced exons are conserved between human and mouse', Genome Research, Vol. 13, No. 7, pp. 1631-1637.
    • (2003) Genome Research , vol.13 , Issue.7 , pp. 1631-1637
    • Sorek, R.1    Ast, G.2
  • 30
    • 4444291467 scopus 로고    scopus 로고
    • A non-EST based method for exon-skipping prediction
    • Sorek, R., Shemesh, R., Cohen, Y., Basechess, O., Ast, G. and Shamir, R. (2004) 'A non-EST based method for exon-skipping prediction', Genome Res., Vol. 14, No. 8, pp. 1617-1623.
    • (2004) Genome Res. , vol.14 , Issue.8 , pp. 1617-1623
    • Sorek, R.1    Shemesh, R.2    Cohen, Y.3    Basechess, O.4    Ast, G.5    Shamir, R.6
  • 31
    • 42149137369 scopus 로고    scopus 로고
    • Accurate splice site prediction using support vector machines
    • Sonnenburg, S., Schweikert, G., Philips, P., Behr, J. and Rätsch, G. (2007) 'Accurate splice site prediction using support vector machines', BMC Bioinformatics, Vol. 8, Suppl. 10, p. 7.
    • (2007) BMC Bioinformatics , vol.8 , Issue.10 SUPPL. , pp. 7
    • Sonnenburg, S.1    Schweikert, G.2    Philips, P.3    Behr, J.4    Rätsch, G.5
  • 32
    • 0348122177 scopus 로고    scopus 로고
    • Prediction and statistical analysis of alternatively spliced exons
    • Thanaraj, T. A. and Stamm, S. (2003) 'Prediction and statistical analysis of alternatively spliced exons', Prog. Mol. Subcell. Biol., Vol. 31, pp. 1-31.
    • (2003) Prog. Mol. Subcell. Biol. , vol.31 , pp. 1-31
    • Thanaraj, T.A.1    Stamm, S.2
  • 34
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter, J. C., Adams, M. D. et al. (2001) 'The sequence of the human genome', Science, Vol. 291, No. 5507, pp. 1304-1351.
    • (2001) Science , vol.291 , Issue.5507 , pp. 1304-1351
    • Venter, J.C.1    Adams, M.D.2
  • 36
    • 32544456772 scopus 로고    scopus 로고
    • Characterization and prediction of alternative splice sites
    • Wang, M. and Marin, A. (2006) 'Characterization and prediction of alternative splice sites', Gene, Vol. 366, No. 2, pp. 219-227.
    • (2006) Gene , vol.366 , Issue.2 , pp. 219-227
    • Wang, M.1    Marin, A.2
  • 37
    • 58049167941 scopus 로고    scopus 로고
    • Exploring alternative splicing features using support vector machine
    • Philadelphia, PA
    • Xia, J., Caragea, D. and Brown, S. (2008) 'Exploring alternative splicing features using support vector machine', Proceedings of IEEE Bionformatics and Biomedicine, Philadelphia, PA, pp. 230-238.
    • (2008) Proceedings of IEEE Bionformatics and Biomedicine , pp. 230-238
    • Xia, J.1    Caragea, D.2    Brown, S.3
  • 39
    • 8144225362 scopus 로고    scopus 로고
    • Variation in sequence and organization of splicing regulatory elements in vertebrate genes
    • Washington DC
    • Yeo, G., Hoon, S., Venkatesh, B. and Burge, C. B. (2002) 'Variation in sequence and organization of splicing regulatory elements in vertebrate genes', Proceedings of the National Academy of Sciences, Vol. 101, No. 44, Washington DC, pp. 15700-15705.
    • (2002) Proceedings of the National Academy of Sciences , vol.101 , Issue.44 , pp. 15700-15705
    • Yeo, G.1    Hoon, S.2    Venkatesh, B.3    Burge, C.B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.