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Volumn 27, Issue 16, 2011, Pages 2181-2186

KvSNP: Accurately predicting the effect of genetic variants in voltage-gated potassium channels

Author keywords

[No Author keywords available]

Indexed keywords

VOLTAGE GATED POTASSIUM CHANNEL;

EID: 79961190441     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr365     Document Type: Article
Times cited : (25)

References (54)
  • 1
    • 0345690174 scopus 로고    scopus 로고
    • Ethnic differences in cardiac potassium channel variants: Implications for genetic susceptibility to sudden cardiac death and genetic testing for congenital long QT syndrome
    • Ackerman,M.J. et al. (2003) Ethnic differences in cardiac potassium channel variants: Implications for genetic susceptibility to sudden cardiac death and genetic testing for congenital long QT syndrome. Mayo Clin. Proc., 78, 1479-1487.
    • (2003) Mayo Clin. Proc. , vol.78 , pp. 1479-1487
    • Ackerman, M.J.1
  • 2
    • 17844392864 scopus 로고    scopus 로고
    • Combining prediction of secondary structure and solvent accessibility in proteins
    • Adamczak,R. et al. (2005) Combining prediction of secondary structure and solvent accessibility in proteins. Proteins, 59, 467-475.
    • (2005) Proteins , vol.59 , pp. 467-475
    • Adamczak, R.1
  • 3
    • 0344737581 scopus 로고    scopus 로고
    • Pharmacogenetic considerations in diseases of cardiac ion channels
    • Anantharam,A. et al. (2003) Pharmacogenetic considerations in diseases of cardiac ion channels. J. Pharmacol. Exp. Ther., 307, 831-838.
    • (2003) J. Pharmacol. Exp. Ther. , vol.307 , pp. 831-838
    • Anantharam, A.1
  • 4
    • 33646372461 scopus 로고    scopus 로고
    • Amino acid size, charge, hydropathy indices and matrices for protein structure analysis
    • Biro,J.C. (2006) Amino acid size, charge, hydropathy indices and matrices for protein structure analysis. Theor. Biol. Med. Model., 3, 15.
    • (2006) Theor. Biol. Med. Model. , vol.3 , pp. 15
    • Biro, J.C.1
  • 5
    • 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
  • 6
    • 0032997217 scopus 로고    scopus 로고
    • The essence of SNPs
    • Brookes,A.J. (1999) The essence of SNPs. Gene, 234, 177.
    • (1999) Gene , vol.234 , pp. 177
    • Brookes, A.J.1
  • 7
    • 77749292124 scopus 로고    scopus 로고
    • Tetramerization domain mutations in KCNA5 affect channel kinetics and cause abnormal trafficking patterns
    • Burg,E.D. et al. (2010) Tetramerization domain mutations in KCNA5 affect channel kinetics and cause abnormal trafficking patterns. Am. J. Physiol. Cell Physiol., 298, C496-C509.
    • (2010) Am. J. Physiol. Cell Physiol. , vol.298
    • Burg, E.D.1
  • 8
    • 67749137351 scopus 로고    scopus 로고
    • Functional annotations improve the predictive score of human disease-related mutations in proteins
    • Calabrese,R. et al. (2009) Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum. Mutat., 30, 1237-1244.
    • (2009) Hum. Mutat. , vol.30 , pp. 1237-1244
    • Calabrese, R.1
  • 9
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • Capra,J.A. and Singh,M. (2007) Predicting functionally important residues from sequence conservation. Bioinformatics, 23, 1875-1882.
    • (2007) Bioinformatics , vol.23 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 10
    • 34147100153 scopus 로고    scopus 로고
    • Deleterious SNP prediction: be mindful of your training data!
    • Care,M.A. et al. (2007) Deleterious SNP prediction: be mindful of your training data! Bioinformatics, 23, 664-672.
    • (2007) Bioinformatics , vol.23 , pp. 664-672
    • Care, M.A.1
  • 11
    • 2442694043 scopus 로고    scopus 로고
    • Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms
    • Clifford,R.J. et al. (2004) Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics, 20, 1006.
    • (2004) Bioinformatics , vol.20 , pp. 1006
    • Clifford, R.J.1
  • 12
    • 24644515300 scopus 로고    scopus 로고
    • KCNH2-K897T is a genetic modifier of latent congenital long QT syndrome
    • Crotti,L. et al. (2005) KCNH2-K897T is a genetic modifier of latent congenital long QT syndrome. Circulation, 112, 1251-1258.
    • (2005) Circulation , vol.112 , pp. 1251-1258
    • Crotti, L.1
  • 13
    • 70349847872 scopus 로고    scopus 로고
    • Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0
    • Dehouck,Y. et al. (2009) Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics, 25, 2537-2543.
    • (2009) Bioinformatics , vol.25 , pp. 2537-2543
    • Dehouck, Y.1
  • 14
    • 53749096681 scopus 로고    scopus 로고
    • Improving position-specific predictions of protein functional sites using phylogenetic motifs
    • Dukka Bahadur,K.C. and Livesay,D.R. (2008) Improving position-specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics, 24, 2308-2316.
    • (2008) Bioinformatics , vol.24 , pp. 2308-2316
    • Dukka Bahadur, K.C.1    Livesay, D.R.2
  • 15
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 16
    • 53649095314 scopus 로고    scopus 로고
    • Prepare for the deluge
    • Editorial
    • Editorial (2008) Prepare for the deluge. Nat. Biotechnol., 26, 1099-1099.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1099-11099
  • 17
    • 77949330477 scopus 로고    scopus 로고
    • Sequence and structural analysis of binding site residues in protein-protein complexes
    • Gromiha,M.M. et al. (2010) Sequence and structural analysis of binding site residues in protein-protein complexes. Int. J. Biol. Macromol., 46, 187-192.
    • (2010) Int. J. Biol. Macromol. , vol.46 , pp. 187-192
    • Gromiha, M.M.1
  • 18
    • 85065703189 scopus 로고    scopus 로고
    • Correlation-based feature selection for discrete and numeric class machine learning
    • Morgan Kaufmann Publishers Inc., San Francisco, CA, USA
    • Hall,M. (2000) Correlation-based feature selection for discrete and numeric class machine learning. In ICML '00: Proceedings of the Seventeenth International Conference on Machine Learning, Morgan Kaufmann Publishers Inc., San Francisco, CA, USA, pp. 359-366.
    • (2000) ICML '00: Proceedings of the Seventeenth International Conference on Machine Learning , pp. 359-366
    • Hall, M.1
  • 19
    • 76749092270 scopus 로고    scopus 로고
    • The WEKAData Mining Software: an update
    • Hall,M. et al. (2009) The WEKAData Mining Software: an update. SIGKDD Expl., 11, 10-18.
    • (2009) SIGKDD Expl. , vol.11 , pp. 10-18
    • Hall, M.1
  • 20
    • 48249113374 scopus 로고    scopus 로고
    • Evolutionary analyses of KCNQ1 and HERG voltage-gated potassium channel sequences reveal location-specific susceptibility and augmented chemical severities of arrhythmogenic mutations
    • Jackson,H. and Accili,E. (2008) Evolutionary analyses of KCNQ1 and HERG voltage-gated potassium channel sequences reveal location-specific susceptibility and augmented chemical severities of arrhythmogenic mutations. BMC Evol. Biol., 8, 188.
    • (2008) BMC Evol. Biol. , vol.8 , pp. 188
    • Jackson, H.1    Accili, E.2
  • 21
    • 33750578872 scopus 로고    scopus 로고
    • Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy
    • Jiang,R. et al. (2006) Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinformatics, 7, 417.
    • (2006) BMC Bioinformatics , vol.7 , pp. 417
    • Jiang, R.1
  • 22
    • 34547765932 scopus 로고    scopus 로고
    • Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations
    • Jiang,R. et al. (2007) Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations. Am. J. Hum. Genet., 81, 346-360.
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 346-360
    • Jiang, R.1
  • 24
    • 22544461665 scopus 로고    scopus 로고
    • Susceptibility genes and modifiers for cardiac arrhythmias
    • Kääb,S. and Schulze-Bahr,E. (2005) Susceptibility genes and modifiers for cardiac arrhythmias. Cardiovas. Res., 67, 397-413.
    • (2005) Cardiovas. Res. , vol.67 , pp. 397-413
    • Kääb, S.1    Schulze-Bahr, E.2
  • 25
    • 0036768621 scopus 로고    scopus 로고
    • Genetics of epilepsy: current status and perspectives
    • Kaneko,S. et al. (2002) Genetics of epilepsy: current status and perspectives. Neurosci. Res., 44, 11-30.
    • (2002) Neurosci. Res. , vol.44 , pp. 11-30
    • Kaneko, S.1
  • 26
    • 70449359365 scopus 로고    scopus 로고
    • Genetic testing for long-QT syndrome: distinguishing pathogenic mutations from benign variants
    • Kapa,S. et al. (2009) Genetic testing for long-QT syndrome: distinguishing pathogenic mutations from benign variants. Circulation, 120, 1752-1760.
    • (2009) Circulation , vol.120 , pp. 1752-1760
    • Kapa, S.1
  • 27
    • 0344033683 scopus 로고    scopus 로고
    • A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
    • Krishnan,V.G. and Westhead,D.R. (2003) A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics, 19, 2199-2209.
    • (2003) Bioinformatics , vol.19 , pp. 2199-2209
    • Krishnan, V.G.1    Westhead, D.R.2
  • 28
    • 0033524936 scopus 로고    scopus 로고
    • KCNQ4, a novel potassium channel expressed in sensory outer hair cells, is mutated in dominant deafness
    • Kubisch,C. et al. (1999) KCNQ4, a novel potassium channel expressed in sensory outer hair cells, is mutated in dominant deafness. Cell, 96, 437.
    • (1999) Cell , vol.96 , pp. 437
    • Kubisch, C.1
  • 29
    • 36248982122 scopus 로고    scopus 로고
    • Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment
    • Long,S.B. et al. (2007) Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature, 450, 376-382.
    • (2007) Nature , vol.450 , pp. 376-382
    • Long, S.B.1
  • 30
    • 32444435135 scopus 로고    scopus 로고
    • SIDS: genetic and environmental influences may cause arrhythmia in this silent killer
    • Makielski,J.C. (2006) SIDS: genetic and environmental influences may cause arrhythmia in this silent killer. J. Clin. Investig., 116, 297-299.
    • (2006) J. Clin. Investig. , vol.116 , pp. 297-299
    • Makielski, J.C.1
  • 31
    • 4143051195 scopus 로고    scopus 로고
    • Comparison of site-specific rate-inference methods for protein sequences: empirical bayesian methods are superior
    • Mayrose,I. et al. (2004) Comparison of site-specific rate-inference methods for protein sequences: empirical bayesian methods are superior. Mol. Biol. Evol., 21, 1781-1791.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1781-1791
    • Mayrose, I.1
  • 32
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • Ng,P. and Henikoff,S. (2001) Predicting deleterious amino acid substitutions. Genome Res., 11, 863-874.
    • (2001) Genome Res. , vol.11 , pp. 863-874
    • Ng, P.1    Henikoff, S.2
  • 33
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: predicting amino acid changes that affect protein function
    • Ng,P.C. and Henikoff,S. (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res., 31, 3812-3814.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 35
    • 33746257526 scopus 로고    scopus 로고
    • Chronic neuromyotonia as a phenotypic variation associated with a new mutation in the;KCNA1; gene
    • Poujois,A. et al. (2006) Chronic neuromyotonia as a phenotypic variation associated with a new mutation in the;KCNA1; gene. J. Neurol., 253, 957-959.
    • (2006) J. Neurol. , vol.253 , pp. 957-959
    • Poujois, A.1
  • 37
    • 0036713510 scopus 로고    scopus 로고
    • Human non-synonymous SNPs: Server and survey
    • Ramensky,V. et al. (2002) Human non-synonymous SNPs: Server and survey. Nucleic Acids Res., 30, 3894-3900.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3894-3900
    • Ramensky, V.1
  • 38
    • 34250618309 scopus 로고    scopus 로고
    • Function of Kv1.5 channels and genetic variations of KCNA5 in patients with idiopathic pulmonary arterial hypertension
    • Remillard,C.V. et al. (2007) Function of Kv1.5 channels and genetic variations of KCNA5 in patients with idiopathic pulmonary arterial hypertension. Am. J. Physiol. Cell Physiol., 292, C1837-C1853.
    • (2007) Am. J. Physiol. Cell Physiol. , vol.292
    • Remillard, C.V.1
  • 39
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 40
    • 0031945847 scopus 로고    scopus 로고
    • Three novel KCNA1 mutations in episodic ataxia type I families
    • Scheffer,H. et al. (1998) Three novel KCNA1 mutations in episodic ataxia type I families. Hum. Genet., 102, 464-466.
    • (1998) Hum. Genet. , vol.102 , pp. 464-466
    • Scheffer, H.1
  • 41
    • 0242635451 scopus 로고    scopus 로고
    • How really rare are rare diseases?: The intriguing case of independent compound mutations in the long QT syndrome
    • Schwartz, P.J. et al. (2003) How really rare are rare diseases?: The intriguing case of independent compound mutations in the long QT syndrome. J. Cardiovas. Electrophysiol., 14, 1120.
    • (2003) J. Cardiovas. Electrophysiol. , vol.14 , pp. 1120
    • Schwartz, P.J.1
  • 42
    • 41449086438 scopus 로고    scopus 로고
    • The primary arrhythmia syndromes: Samemutation, different manifestations. Are we starting to understand why?
    • Scicluna,B.P. et al. (2008) The primary arrhythmia syndromes: Samemutation, different manifestations. Are we starting to understand why? J. Cardiovas. Electrophysiol., 19, 445-452.
    • (2008) J. Cardiovas. Electrophysiol. , vol.19 , pp. 445-452
    • Scicluna, B.P.1
  • 43
    • 0035173378 scopus 로고    scopus 로고
    • dbSNP: the NCBI database of genetic variation
    • Sherry,S.T. et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 308-311
    • Sherry, S.T.1
  • 44
    • 38549119530 scopus 로고    scopus 로고
    • MutDB: update on development of tools for the biochemical analysis of genetic variation
    • Singh,A. et al. (2008) MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res., 36, D815-D819.
    • (2008) Nucleic Acids Res. , vol.36
    • Singh, A.1
  • 45
    • 0034609531 scopus 로고    scopus 로고
    • Spectrum of mutations in long-QT syndrome genes: KVLQT1, HERG, SCN5A, KCNE1, and KCNE2
    • Splawski,I. et al. (2000) Spectrum of mutations in long-QT syndrome genes: KVLQT1, HERG, SCN5A, KCNE1, and KCNE2. Circulation, 102, 1178-1185.
    • (2000) Circulation , vol.102 , pp. 1178-1185
    • Splawski, I.1
  • 46
    • 77955080355 scopus 로고    scopus 로고
    • KvDB; mining and mapping sequence variants in voltage-gated potassium channels
    • Stead,L.F. et al. (2010) KvDB; mining and mapping sequence variants in voltage-gated potassium channels. Hum. Mutat., 31, 908-917.
    • (2010) Hum. Mutat. , vol.31 , pp. 908-917
    • Stead, L.F.1
  • 47
    • 77953446523 scopus 로고    scopus 로고
    • The Human Gene Mutation Database: 2008 update
    • Stenson,P.D. et al. (2009) The Human Gene Mutation Database: 2008 update. Genome Med., 1, 13.
    • (2009) Genome Med. , vol.1 , pp. 13
    • Stenson, P.D.1
  • 48
    • 0035869223 scopus 로고    scopus 로고
    • Prediction of deleterious human alleles
    • Sunyaev,S. et al. (2001) Prediction of deleterious human alleles. Hum. Mol. Genet., 10, 591-597.
    • (2001) Hum. Mol. Genet. , vol.10 , pp. 591-597
    • Sunyaev, S.1
  • 49
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Consortium
    • The ENCODE Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799.
    • (2007) Nature , vol.447 , pp. 799
  • 50
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap Project
    • The International HapMap Consortium
    • The International HapMap Consortium (2003) The International HapMap Project. Nature, 426, 789.
    • (2003) Nature , vol.426 , pp. 789
  • 51
    • 58149191270 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) 2009
    • The UniProt Consortium
    • The UniProt Consortium (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
    • (2009) Nucleic Acids Res. , vol.37
  • 52
    • 36448935249 scopus 로고    scopus 로고
    • Accurate prediction of deleterious protein kinase polymorphisms
    • Torkamani,A. and Schork,N.J. (2007) Accurate prediction of deleterious protein kinase polymorphisms. Bioinformatics, 23, 2918-2925.
    • (2007) Bioinformatics , vol.23 , pp. 2918-2925
    • Torkamani, A.1    Schork, N.J.2
  • 53
    • 33645809963 scopus 로고    scopus 로고
    • Sudden infant death syndrome and long QT syndrome: an epidemiological and genetic study
    • Wedekind,H. et al. (2006) Sudden infant death syndrome and long QT syndrome: an epidemiological and genetic study. Int. J. Legal Med., 120, 129-137.
    • (2006) Int. J. Legal Med. , vol.120 , pp. 129-137
    • Wedekind, H.1
  • 54
    • 32044453591 scopus 로고    scopus 로고
    • Identification and analysis of deleterious human SNPs
    • Yue,P. and Moult,J. (2006) Identification and analysis of deleterious human SNPs. J. Mol. Biol., 356, 1263.
    • (2006) J. Mol. Biol. , vol.356 , pp. 1263
    • Yue, P.1    Moult, J.2


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