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Volumn 42, Issue 22, 2014, Pages 13534-13544

In silico prediction of splice-altering single nucleotide variants in the human genome

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; AREA UNDER THE CURVE; ARTICLE; COMPUTER MODEL; CONSENSUS SEQUENCE; CONTROLLED STUDY; GENE SEQUENCE; GENETIC PROCEDURES; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; MAXENTSCAN MODEL; POSITION WEIGHT MATRIX; PREDICTION; PRIORITY JOURNAL; RANDOM FOREST; SINGLE NUCLEOTIDE VARIANT WITHIN SPLICING CONSENSUS REGION; TUMOR GENE; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; GENOMICS; PROCEDURES; RNA SPLICING; VALIDATION STUDY;

EID: 84926503617     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1206     Document Type: Article
Times cited : (363)

References (58)
  • 1
    • 0344622123 scopus 로고
    • Spliced segments at the 5' terminus of adenovirus 2 late mRNA
    • Berget, S. M., Moore, C. and Sharp, P. A. (1977) Spliced segments at the 5' terminus of adenovirus 2 late mRNA. Proc. Natl. Acad. Sci. U. S. A., 74, 3171-3175.
    • (1977) Proc. Natl. Acad. Sci. U. S. A. , vol.74 , pp. 3171-3175
    • Berget, S.M.1    Moore, C.2    Sharp, P.A.3
  • 2
    • 0017688583 scopus 로고
    • An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA
    • Chow, L. T., Gelinas, R. E., Broker, T. R. and Roberts, R. J. (1977) An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA. Cell, 12, 1-8.
    • (1977) Cell , vol.12 , pp. 1-8
    • Chow, L.T.1    Gelinas, R.E.2    Broker, T.R.3    Roberts, R.J.4
  • 3
    • 0037443035 scopus 로고    scopus 로고
    • Pre-mRNA splicing and human disease
    • Faustino, N. A. and Cooper, T. A. (2003) Pre-mRNA splicing and human disease. Genes Dev., 17, 419-437.
    • (2003) Genes Dev. , vol.17 , pp. 419-437
    • Faustino, N.A.1    Cooper, T.A.2
  • 4
    • 34548758543 scopus 로고    scopus 로고
    • Splicing in disease: Disruption of the splicing code and the decoding machinery
    • Wang, G. S. and Cooper, T. A. (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nat. Rev. Genet., 8, 749-761.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 749-761
    • Wang, G.S.1    Cooper, T.A.2
  • 5
    • 42449133852 scopus 로고    scopus 로고
    • Alternative splicing in disease
    • Orengo, J. P. and Cooper, T. A. (2007) Alternative splicing in disease. Adv. Exp. Med. Biol., 623, 212-223.
    • (2007) Adv. Exp. Med. Biol. , vol.623 , pp. 212-223
    • Orengo, J.P.1    Cooper, T.A.2
  • 6
    • 0013394889 scopus 로고    scopus 로고
    • Mechanisms of alternative pre-messenger RNA splicing
    • Black, D. L. (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem., 72, 291-336.
    • (2003) Annu. Rev. Biochem. , vol.72 , pp. 291-336
    • Black, D.L.1
  • 7
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan, Q., Shai, O., Lee, L. J., Frey, B. J. and Blencowe, B. J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
    • (2008) Nat. Genet. , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 9
    • 79960594889 scopus 로고    scopus 로고
    • Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes
    • Lim, K. H., Ferraris, L., Filloux, M. E., Raphael, B. J. and Fairbrother, W. G. (2011) Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc. Natl. Acad. Sci. U. S. A., 108, 11093-11098.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 11093-11098
    • Lim, K.H.1    Ferraris, L.2    Filloux, M.E.3    Raphael, B.J.4    Fairbrother, W.G.5
  • 10
    • 79960607075 scopus 로고    scopus 로고
    • Loss of exon identity is a common mechanism of human inherited disease
    • Sterne-Weiler, T., Howard, J., Mort, M., Cooper, D. N. and Sanford, J. R. (2011) Loss of exon identity is a common mechanism of human inherited disease. Genome Res., 21, 1563-1571.
    • (2011) Genome Res. , vol.21 , pp. 1563-1571
    • Sterne-Weiler, T.1    Howard, J.2    Mort, M.3    Cooper, D.N.4    Sanford, J.R.5
  • 12
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • Yeo, G. and Burge, C. B. (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
    • (2004) J. Comput. Biol. , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 13
    • 0347988093 scopus 로고    scopus 로고
    • Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: Maximum entropy estimates of splice junction strengths
    • Eng, L., Coutinho, G., Nahas, S., Yeo, G., Tanouye, R., Babaei, M., Dork, T., Burge, C. and Gatti, R. A. (2004) Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths. Hum. Mutat., 23, 67-76.
    • (2004) Hum. Mutat. , vol.23 , pp. 67-76
    • Eng, L.1    Coutinho, G.2    Nahas, S.3    Yeo, G.4    Tanouye, R.5    Babaei, M.6    Dork, T.7    Burge, C.8    Gatti, R.A.9
  • 14
    • 0042242582 scopus 로고    scopus 로고
    • ESEfinder: A web resource to identify exonic splicing enhancers
    • Cartegni, L., Wang, J., Zhu, Z., Zhang, M. Q. and Krainer, A. R. (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res., 31, 3568-3571.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3568-3571
    • Cartegni, L.1    Wang, J.2    Zhu, Z.3    Zhang, M.Q.4    Krainer, A.R.5
  • 16
    • 84903752213 scopus 로고    scopus 로고
    • In silico tools for splicing defect prediction: A survey from the viewpoint of end users
    • Jian, X., Boerwinkle, E. and Liu, X. (2014) In silico tools for splicing defect prediction: a survey from the viewpoint of end users. Genet. Med., 16, 497-503.
    • (2014) Genet. Med. , vol.16 , pp. 497-503
    • Jian, X.1    Boerwinkle, E.2    Liu, X.3
  • 17
    • 0001468848 scopus 로고    scopus 로고
    • Gesteland, RF, Cech, TR and Atkins, JF eds, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Burge, C. B., Tuschl, T. and Sharp, P. A. (1999) In: Gesteland, RF, Cech, TR and Atkins, JF (eds). The RNA World. 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 525-560.
    • (1999) The RNA World , pp. 525-560
    • Burge, C.B.1    Tuschl, T.2    Sharp, P.A.3
  • 20
    • 84862185370 scopus 로고    scopus 로고
    • SpliceDisease database: Linking RNA splicing and disease
    • Wang, J., Zhang, J., Li, K., Zhao, W. and Cui, Q. (2012) SpliceDisease database: linking RNA splicing and disease. Nucleic Acids Res., 40, D1055-D1059.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D1055-D1059
    • Wang, J.1    Zhang, J.2    Li, K.3    Zhao, W.4    Cui, Q.5
  • 21
    • 78651268938 scopus 로고    scopus 로고
    • DBASS3 and DBASS5: Databases of aberrant 3'- and 5'-splice sites
    • Buratti, E., Chivers, M., Hwang, G. and Vorechovsky, I. (2011) DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites. Nucleic Acids Res., 39, D86-D91.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D86-D91
    • Buratti, E.1    Chivers, M.2    Hwang, G.3    Vorechovsky, I.4
  • 22
    • 84863873006 scopus 로고    scopus 로고
    • Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants
    • Houdayer, C., Caux-Moncoutier, V., Krieger, S., Barrois, M., Bonnet, F., Bourdon, V., Bronner, M., Buisson, M., Coulet, F., Gaildrat, P. et al. (2012) Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum. Mutat., 33, 1228-1238.
    • (2012) Hum. Mutat. , vol.33 , pp. 1228-1238
    • Houdayer, C.1    Caux-Moncoutier, V.2    Krieger, S.3    Barrois, M.4    Bonnet, F.5    Bourdon, V.6    Bronner, M.7    Buisson, M.8    Coulet, F.9    Gaildrat, P.10
  • 25
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data
    • Wang, K., Li, M. and Hakonarson, H. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, e164.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 26
    • 0023651307 scopus 로고
    • RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression
    • Shapiro, M. B. and Senapathy, P. (1987) RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res., 15, 7155-7174.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 7155-7174
    • Shapiro, M.B.1    Senapathy, P.2
  • 28
    • 0035282695 scopus 로고    scopus 로고
    • GeneSplicer: A new computational method for splice site prediction
    • Pertea, M., Lin, X. and Salzberg, S. L. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res., 29, 1185-1190.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1185-1190
    • Pertea, M.1    Lin, X.2    Salzberg, S.L.3
  • 30
    • 0025744474 scopus 로고
    • Prediction of human mRNA donor and acceptor sites from the DNA sequence
    • Brunak, S., Engelbrecht, J. and Knudsen, S. (1991) Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol., 220, 49-65.
    • (1991) J. Mol. Biol. , vol.220 , pp. 49-65
    • Brunak, S.1    Engelbrecht, J.2    Knudsen, S.3
  • 31
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 32
    • 2442690356 scopus 로고    scopus 로고
    • Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
    • Brendel, V., Xing, L. and Zhu, W. (2004) Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics, 20, 1157-1169.
    • (2004) Bioinformatics , vol.20 , pp. 1157-1169
    • Brendel, V.1    Xing, L.2    Zhu, W.3
  • 33
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett, T. (2006) An introduction to ROC analysis. Pattern Recognit. Lett., 27, 861-874.
    • (2006) Pattern Recognit. Lett. , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 36
    • 0031211090 scopus 로고    scopus 로고
    • A decision-theoretic generalization of on-line learning and an application to boosting
    • Freund, Y. and Schapire, R. E. (1997) A decision-theoretic generalization of on-line learning and an application to boosting. J. Comput. Syst. Sci., 55, 119-139.
    • (1997) J. Comput. Syst. Sci. , vol.55 , pp. 119-139
    • Freund, Y.1    Schapire, R.E.2
  • 37
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. (2001) Random forests. Mach. Learn., 45, 5-32.
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 39
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • Liaw, A. and Wiener, M. (2002) Classification and regression by randomForest. R. News, 2, 18-22.
    • (2002) R. News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 41
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M. and Shendure, J. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet., 46, 310-315.
    • (2014) Nat. Genet. , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 44
    • 84876527918 scopus 로고    scopus 로고
    • Cancer genome-sequencing study design
    • Mwenifumbo, J. C. and Marra, M. A. (2013) Cancer genome-sequencing study design. Nat. Rev. Genet., 14, 321-332.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 321-332
    • Mwenifumbo, J.C.1    Marra, M.A.2
  • 45
    • 7444220147 scopus 로고    scopus 로고
    • Aberrant and alternative splicing in cancer
    • Venables, J. P. (2004) Aberrant and alternative splicing in cancer. Cancer Res., 64, 7647-7654.
    • (2004) Cancer Res. , vol.64 , pp. 7647-7654
    • Venables, J.P.1
  • 46
    • 33746927884 scopus 로고    scopus 로고
    • The connection between splicing and cancer
    • Srebrow, A. and Kornblihtt, A. R. (2006) The connection between splicing and cancer. J. Cell Sci., 119, 2635-2641.
    • (2006) J. Cell Sci. , vol.119 , pp. 2635-2641
    • Srebrow, A.1    Kornblihtt, A.R.2
  • 47
    • 84896366070 scopus 로고    scopus 로고
    • Synonymous mutations frequently act as driver mutations in human cancers
    • Supek, F., Minana, B., Valcarcel, J., Gabaldon, T. and Lehner, B. (2014) Synonymous mutations frequently act as driver mutations in human cancers. Cell, 156, 1324-1335.
    • (2014) Cell , vol.156 , pp. 1324-1335
    • Supek, F.1    Minana, B.2    Valcarcel, J.3    Gabaldon, T.4    Lehner, B.5
  • 49
    • 79960763462 scopus 로고    scopus 로고
    • Dbnsfp: A lightweight database of human nonsynonymous SNPs and their functional predictions
    • Liu, X., Jian, X. and Boerwinkle, E. (2011) dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum. Mutat., 32, 894-899.
    • (2011) Hum. Mutat. , vol.32 , pp. 894-899
    • Liu, X.1    Jian, X.2    Boerwinkle, E.3
  • 50
    • 84881613239 scopus 로고    scopus 로고
    • Dbnsfp v2.0: A database of human non-synonymous SNVs and their functional predictions and annotations
    • Liu, X., Jian, X. and Boerwinkle, E. (2013) dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat., 34, E2393-E2402.
    • (2013) Hum. Mutat. , vol.34 , pp. E2393-E2402
    • Liu, X.1    Jian, X.2    Boerwinkle, E.3
  • 51
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • Ozsolak, F. and Milos, P. M. (2011) RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet., 12, 87-98.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 52
    • 84865676796 scopus 로고    scopus 로고
    • Detection and quantification of alternative splicing variants using RNA-seq
    • Bryant, D. W. Jr, Priest, H. D. and Mockler, T. C. (2012) Detection and quantification of alternative splicing variants using RNA-seq. Methods Mol. Biol., 883, 97-110.
    • (2012) Methods Mol. Biol. , vol.883 , pp. 97-110
    • Bryant, D.W.1    Priest, H.D.2    Mockler, T.C.3
  • 54
    • 84979844527 scopus 로고    scopus 로고
    • Validation of predicted mRNA splicing mutations using high-throughput transcriptome data
    • Viner, C., Dorman, S. N., Shirley, B. C. and Rogan, P. K. (2014) Validation of predicted mRNA splicing mutations using high-throughput transcriptome data. F1000Res, 3, 8.
    • (2014) F1000Res , vol.3 , pp. 8
    • Viner, C.1    Dorman, S.N.2    Shirley, B.C.3    Rogan, P.K.4
  • 55
    • 26944453614 scopus 로고    scopus 로고
    • Splicing in action: Assessing disease causing sequence changes
    • Baralle, D. and Baralle, M. (2005) Splicing in action: assessing disease causing sequence changes. J. Med. Genet., 42, 737-748.
    • (2005) J. Med. Genet. , vol.42 , pp. 737-748
    • Baralle, D.1    Baralle, M.2
  • 56
    • 68249121529 scopus 로고    scopus 로고
    • Missed threads. The impact of pre-mRNA splicing defects on clinical practice
    • Baralle, D., Lucassen, A. and Buratti, E. (2009) Missed threads. The impact of pre-mRNA splicing defects on clinical practice. EMBO Rep., 10, 810-816.
    • (2009) EMBO Rep. , vol.10 , pp. 810-816
    • Baralle, D.1    Lucassen, A.2    Buratti, E.3
  • 58
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • Fairbrother, W. G., Yeh, R. F., Sharp, P. A. and Burge, C. B. (2002) Predictive identification of exonic splicing enhancers in human genes. Science, 297, 1007-1013.
    • (2002) Science , vol.297 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.F.2    Sharp, P.A.3    Burge, C.B.4


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