메뉴 건너뛰기




Volumn 16, Issue 7, 2014, Pages 497-503

In silico tools for splicing defect prediction: A survey from the viewpoint of end users

Author keywords

Bioinformatics; End user; In silico prediction tool; Medical genetics; Splicing consensus region; Splicing mutation

Indexed keywords

ALGORITHM; BIOINFORMATICS; COMPUTER MODEL; CONSENSUS; HUMAN; MEDICAL GENETICS; PREDICTION; REVIEW; RNA SPLICING; SPLICING DEFECT; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETIC VARIABILITY; GENETICS; PROCEDURES;

EID: 84903752213     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2013.176     Document Type: Review
Times cited : (113)

References (42)
  • 1
    • 0344622123 scopus 로고
    • Spliced segments at the 5' terminus of adenovirus 2 late mRNA
    • Berget SM, Moore C, Sharp PA. Spliced segments at the 5' terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci USA 1977;74:3171-3175.
    • (1977) Proc Natl Acad Sci USA , 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 LT, Gelinas RE, Broker TR, Roberts RJ. An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA. Cell 1977;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
    • 0019363396 scopus 로고
    • Organization and expression of eucaryotic split genes coding for proteins
    • Breathnach R, Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem 1981;50:349-383.
    • (1981) Annu Rev Biochem , vol.50 , pp. 349-383
    • Breathnach, R.1    Chambon, P.2
  • 4
    • 0023651307 scopus 로고
    • RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression
    • Shapiro MB, Senapathy P. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res 1987;15:7155-7174.
    • (1987) Nucleic Acids Res , vol.15 , pp. 7155-7174
    • Shapiro, M.B.1    Senapathy, P.2
  • 5
    • 0001468848 scopus 로고    scopus 로고
    • Splicing of precursors to mRNAs by the spliceosomes
    • Gesteland RF, Cech TR, Atkins JF (eds). Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York
    • Burge CB, Tuschl T, Sharp PA. Splicing of precursors to mRNAs by the spliceosomes. In: Gesteland RF, Cech TR, Atkins JF (eds). The RNA World. 2nd edn. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York, 1999:525-560.
    • (1999) The RNA World. 2nd Edn , pp. 525-560
    • Burge, C.B.1    Tuschl, T.2    Sharp, P.A.3
  • 6
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: Exonic mutations that affect splicing
    • Cartegni L, Chew SL, Krainer AR. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002;3:285- 298.
    • (2002) Nat Rev Genet , vol.3 , pp. 285-298
    • Cartegni, L.1    Chew, S.L.2    Krainer, A.R.3
  • 7
    • 0030707797 scopus 로고    scopus 로고
    • Nonsyndromic deafness DFNA1 associated with mutation of a human homolog of the Drosophila gene diaphanous
    • Lynch ED, Lee MK, Morrow JE, Welcsh PL, León PE, King MC. Nonsyndromic deafness DFNA1 associated with mutation of a human homolog of the Drosophila gene diaphanous. Science 1997;278:1315-1318.
    • (1997) Science , vol.278 , pp. 1315-1318
    • Lynch, E.D.1    Lee, M.K.2    Morrow, J.E.3    Welcsh, P.L.4    León, P.E.5    King, M.C.6
  • 8
    • 0028797783 scopus 로고
    • Identification and characterization of a spinal muscular atrophy-determining gene
    • Lefebvre S, Bürglen L, Reboullet S, et al. Identification and characterization of a spinal muscular atrophy-determining gene. Cell 1995;80:155-165.
    • (1995) Cell , vol.80 , pp. 155-165
    • Lefebvre, S.1    Bürglen, L.2    Reboullet, S.3
  • 9
    • 0036544654 scopus 로고    scopus 로고
    • Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1
    • Cartegni L, Krainer AR. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat Genet 2002;30:377-384.
    • (2002) Nat Genet , vol.30 , pp. 377-384
    • Cartegni, L.1    Krainer, A.R.2
  • 11
    • 34548758543 scopus 로고    scopus 로고
    • Splicing in disease: Disruption of the splicing code and the decoding machinery
    • Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007;8:749-761.
    • (2007) Nat Rev Genet , vol.8 , pp. 749-761
    • Wang, G.S.1    Cooper, T.A.2
  • 13
    • 0026794668 scopus 로고
    • The mutational spectrum of single basepair substitutions in mRNA splice junctions of human genes: Causes and consequences
    • Krawczak M, Reiss J, Cooper DN. The mutational spectrum of single basepair substitutions in mRNA splice junctions of human genes: causes and consequences. Hum Genet 1992;90:41-54.
    • (1992) Hum Genet , vol.90 , pp. 41-54
    • Krawczak, M.1    Reiss, J.2    Cooper, D.N.3
  • 14
    • 79960594889 scopus 로고    scopus 로고
    • Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes
    • Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG. Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci USA 2011;108:11093-11098.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 11093-11098
    • Lim, K.H.1    Ferraris, L.2    Filloux, M.E.3    Raphael, B.J.4    Fairbrother, W.G.5
  • 15
  • 16
    • 68249121529 scopus 로고    scopus 로고
    • Missed threads the impact of pre-mRNA splicing defects on clinical practice
    • Baralle D, Lucassen A, Buratti E. Missed threads. The impact of pre-mRNA splicing defects on clinical practice. EMBO Rep 2009;10:810-816.
    • (2009) EMBO Rep , vol.10 , pp. 810-816
    • Baralle, D.1    Lucassen, A.2    Buratti, E.3
  • 18
    • 0030787856 scopus 로고    scopus 로고
    • Analysis of donor splice sites in different eukaryotic organisms
    • Rogozin IB, Milanesi L. Analysis of donor splice sites in different eukaryotic organisms. J Mol Evol 1997;45:50-59.
    • (1997) J Mol Evol , vol.45 , pp. 50-59
    • Rogozin, I.B.1    Milanesi, L.2
  • 19
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997;268:78-94.
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 20
    • 0035282695 scopus 로고    scopus 로고
    • GeneSplicer: A new computational method for splice site prediction
    • Pertea M, Lin X, Salzberg SL. GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res 2001;29:1185-1190.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1185-1190
    • Pertea, M.1    Lin, X.2    Salzberg, S.L.3
  • 21
    • 0025744474 scopus 로고
    • Prediction of human mRNA donor and acceptor sites from the DNA sequence
    • Brunak S, Engelbrecht J, Knudsen S. Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol 1991;220:49-65.
    • (1991) J Mol Biol , vol.220 , pp. 49-65
    • Brunak, S.1    Engelbrecht, J.2    Knudsen, S.3
  • 24
    • 2442690356 scopus 로고    scopus 로고
    • Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
    • Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 2004;20:1157-1169.
    • (2004) Bioinformatics , vol.20 , pp. 1157-1169
    • Brendel, V.1    Xing, L.2    Zhu, W.3
  • 25
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 2004;11:377-394.
    • (2004) J Comput Biol , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 26
    • 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, et al. Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths. Hum Mutat 2004;23:67-76.
    • (2004) Hum Mutat , vol.23 , pp. 67-76
    • Eng, L.1    Coutinho, G.2    Nahas, S.3
  • 27
    • 10744224600 scopus 로고    scopus 로고
    • A novel approach to describe a U1 snRNA binding site
    • Freund M, Asang C, Kammler S, et al. A novel approach to describe a U1 snRNA binding site. Nucleic Acids Res 2003;31:6963-6975.
    • (2003) Nucleic Acids Res , vol.31 , pp. 6963-6975
    • Freund, M.1    Asang, C.2    Kammler, S.3
  • 28
    • 17144362174 scopus 로고    scopus 로고
    • Automated splicing mutation analysis by information theory
    • Nalla VK, Rogan PK. Automated splicing mutation analysis by information theory. Hum Mutat 2005;25:334-342.
    • (2005) Hum Mutat , vol.25 , pp. 334-342
    • Nalla, V.K.1    Rogan, P.K.2
  • 29
    • 67349134700 scopus 로고    scopus 로고
    • Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping
    • Divina P, Kvitkovicova A, Buratti E, Vorechovsky I. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet 2009;17:759-765.
    • (2009) Eur J Hum Genet , vol.17 , pp. 759-765
    • Divina, P.1    Kvitkovicova, A.2    Buratti, E.3    Vorechovsky, I.4
  • 30
    • 84859240596 scopus 로고    scopus 로고
    • Spliceman-A computational web server that predicts sequence variations in pre-mRNA splicing
    • Lim KH, Fairbrother WG. Spliceman-a computational web server that predicts sequence variations in pre-mRNA splicing. Bioinformatics 2012;28:1031-1032.
    • (2012) Bioinformatics , vol.28 , pp. 1031-1032
    • Lim, K.H.1    Fairbrother, W.G.2
  • 32
    • 67849092454 scopus 로고    scopus 로고
    • SROOGLE: Webserver for integrative, user-friendly visualization of splicing signals
    • Web Server issue
    • Schwartz S, Hall E, Ast G. SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res 2009;37(Web Server issue):W189-W192.
    • (2009) Nucleic Acids Res , vol.37
    • Schwartz, S.1    Hall, E.2    Ast, G.3
  • 33
    • 79959940492 scopus 로고    scopus 로고
    • Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites
    • Faber K, Glatting KH, Mueller PJ, Risch A, Hotz-Wagenblatt A. Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites. BMC Bioinformatics 2011;12(suppl 4):S2.
    • (2011) BMC Bioinformatics , vol.12 SUPPL. 4
    • Faber, K.1    Glatting, K.H.2    Mueller, P.J.3    Risch, A.4    Hotz-Wagenblatt, A.5
  • 34
    • 84903769542 scopus 로고    scopus 로고
    • Bioinformatics identification of splice site signals and prediction of mutation effects
    • Mohan RM (ed) Global Research Network: Kerala
    • Desmet FO, Hamroun D, Collod-Beroud G, Claustres M, Beroud C. Bioinformatics identification of splice site signals and prediction of mutation effects. In: Mohan RM (ed). Research Advances in Nucleic Acids Research. Global Research Network: Kerala, 2010:1-14.
    • (2010) Research Advances in Nucleic Acids Research , pp. 1-14
    • Desmet, F.O.1    Hamroun, D.2    Collod-Beroud, G.3    Claustres, M.4    Beroud, C.5
  • 35
    • 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, et al. 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 2012;33:1228- 1238.
    • (2012) Hum Mutat , vol.33 , pp. 1228-1238
    • Houdayer, C.1    Caux-Moncoutier, V.2    Krieger, S.3
  • 36
    • 63449100039 scopus 로고    scopus 로고
    • Cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium: Design of prospective meta-analyses of genome-wide association studies from 5 cohorts
    • Psaty BM, O'Donnell CJ, Gudnason V, et al.; CHARGE Consortium. Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium: Design of prospective meta-analyses of genome-wide association studies from 5 cohorts. Circ Cardiovasc Genet 2009;2:73-80.
    • (2009) Circ Cardiovasc Genet , vol.2 , pp. 73-80
    • Psaty, B.M.1    O'Donnell, C.J.2    Gudnason, V.3
  • 37
    • 84903783260 scopus 로고    scopus 로고
    • NIH program explores the use of genomic sequencing in newborn healthcare Accessed 4 September 2013
    • NIH program explores the use of genomic sequencing in newborn healthcare. 2013. http://www.nih.gov/news/health/sep2013/nhgri-04.htm. Accessed4September2013.
    • (2013)
  • 38
    • 46749098393 scopus 로고    scopus 로고
    • Evaluation of in silico splice tools for decision-making in molecular diagnosis
    • Houdayer C, Dehainault C, Mattler C, et al. Evaluation of in silico splice tools for decision-making in molecular diagnosis. Hum Mutat 2008;29:975-982.
    • (2008) Hum Mutat , vol.29 , pp. 975-982
    • Houdayer, C.1    Dehainault, C.2    Mattler, C.3
  • 39
    • 61849159311 scopus 로고    scopus 로고
    • Effects of intronic mutations in the LDLR gene on pre-mRNA splicing: Comparison of wet-lab and bioinformatics analyses
    • Holla OøL, Nakken S, Mattingsdal M, et al. Effects of intronic mutations in the LDLR gene on pre-mRNA splicing: Comparison of wet-lab and bioinformatics analyses. Mol Genet Metab 2009;96:245-252.
    • (2009) Mol Genet Metab , vol.96 , pp. 245-252
    • Holla, Oø.L.1    Nakken, S.2    Mattingsdal, M.3
  • 40
    • 58349088957 scopus 로고    scopus 로고
    • Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs
    • Vreeswijk MP, Kraan JN, van der Klift HM, et al. Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs. Hum Mutat 2009;30:107-114.
    • (2009) Hum Mutat , vol.30 , pp. 107-114
    • Vreeswijk, M.P.1    Kraan, J.N.2    Van Der Klift, H.M.3
  • 41
    • 80053052971 scopus 로고    scopus 로고
    • Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes
    • Théry JC, Krieger S, Gaildrat P, et al. Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes. Eur J Hum Genet 2011;19:1052-1058.
    • (2011) Eur J Hum Genet , vol.19 , pp. 1052-1058
    • Théry, J.C.1    Krieger, S.2    Gaildrat, P.3
  • 42
    • 84874299712 scopus 로고    scopus 로고
    • Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations
    • Colombo M, De Vecchi G, Caleca L, et al. Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations. PLoS ONE 2013;8:e57173.
    • (2013) PLoS ONE , vol.8
    • Colombo, M.1    De Vecchi, G.2    Caleca, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.