메뉴 건너뛰기




Volumn 426, Issue 14, 2014, Pages 2692-2701

SuSPect: Enhanced prediction of single amino acid variant (SAV) phenotype using network features

Author keywords

missense mutation; nsSNP; protein protein interaction; SAV; SuSPect

Indexed keywords

AMINO ACID; PROTEOME;

EID: 84903147593     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2014.04.026     Document Type: Article
Times cited : (180)

References (59)
  • 1
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • The 1000 Genomes Project Consortium
    • The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 2
    • 79951521421 scopus 로고    scopus 로고
    • Progress and promise of genome-wide association studies for human complex trait genetics
    • B.E. Stranger, E.A. Stahl, and T. Raj Progress and promise of genome-wide association studies for human complex trait genetics Genetics 187 2011 367 383
    • (2011) Genetics , vol.187 , pp. 367-383
    • Stranger, B.E.1    Stahl, E.A.2    Raj, T.3
  • 3
    • 77951799158 scopus 로고    scopus 로고
    • Analysis of genetic inheritance in a family quartet by whole-genome sequencing
    • J.C. Roach, G. Glusman, A.F.A. Smit, C.D. Huff, R. Hubley, and P.T. Shannon et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing Science 328 2010 636 639
    • (2010) Science , vol.328 , pp. 636-639
    • Roach, J.C.1    Glusman, G.2    Smit, A.F.A.3    Huff, C.D.4    Hubley, R.5    Shannon, P.T.6
  • 4
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: Predicting amino acid changes that affect protein function
    • P.C. Ng SIFT: predicting amino acid changes that affect protein function Nucleic Acids Res 31 2003 3812 3814
    • (2003) Nucleic Acids Res , vol.31 , pp. 3812-3814
    • Ng, P.C.1
  • 5
    • 34547100092 scopus 로고    scopus 로고
    • SNAP: Predict effect of non-synonymous polymorphisms on function
    • Y. Bromberg, and B. Rost SNAP: predict effect of non-synonymous polymorphisms on function Nucleic Acids Res 35 2007 3823 3835
    • (2007) Nucleic Acids Res , vol.35 , pp. 3823-3835
    • Bromberg, Y.1    Rost, B.2
  • 6
    • 48249136625 scopus 로고    scopus 로고
    • Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms
    • T.M.K. Cheng, Y.-E. Lu, M. Vendruscolo, P. Lio', and T.L. Blundell Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms PLoS Comput Biol 4 2008 e1000135
    • (2008) PLoS Comput Biol , vol.4 , pp. 1000135
    • Cheng, T.M.K.1    Lu, Y.-E.2    Vendruscolo, M.3    Lio, P.4    Blundell, T.L.5
  • 7
    • 67749137351 scopus 로고    scopus 로고
    • Functional annotations improve the predictive score of human disease-related mutations in proteins
    • R. Calabrese, E. Capriotti, P. Fariselli, P.L. Martelli, and R. Casadio Functional annotations improve the predictive score of human disease-related mutations in proteins Hum Mutat 30 2009 1237 1244
    • (2009) Hum Mutat , vol.30 , pp. 1237-1244
    • Calabrese, R.1    Capriotti, E.2    Fariselli, P.3    Martelli, P.L.4    Casadio, R.5
  • 9
    • 79953715693 scopus 로고    scopus 로고
    • Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score Condel
    • A. González-Pérez, and N. López-Bigas Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score Condel Am J Hum Genet 88 2011 440 449
    • (2011) Am J Hum Genet , vol.88 , pp. 440-449
    • González-Pérez, A.1    López-Bigas, N.2
  • 10
    • 84875728496 scopus 로고    scopus 로고
    • Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs)
    • C.M. Yates, and M.J.E. Sternberg Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs) J Mol Biol 425 2013 1274 1286
    • (2013) J Mol Biol , vol.425 , pp. 1274-1286
    • Yates, C.M.1    Sternberg, M.J.E.2
  • 11
    • 19544392545 scopus 로고    scopus 로고
    • Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
    • L. Bao, and Y. Cui Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information Bioinformatics 21 2005 2185 2190
    • (2005) Bioinformatics , vol.21 , pp. 2185-2190
    • Bao, L.1    Cui, Y.2
  • 12
    • 79960029961 scopus 로고    scopus 로고
    • Improving the prediction of disease-related variants using protein three-dimensional structure
    • E. Capriotti, and R.B. Altman Improving the prediction of disease-related variants using protein three-dimensional structure BMC Bioinformatics 12 2011 S3
    • (2011) BMC Bioinformatics , vol.12 , pp. 3
    • Capriotti, E.1    Altman, R.B.2
  • 13
    • 25144523127 scopus 로고    scopus 로고
    • Loss of protein structure stability as a major causative factor in monogenic disease
    • P. Yue, Z. Li, and J. Moult Loss of protein structure stability as a major causative factor in monogenic disease J Mol Biol 353 2005 459 473
    • (2005) J Mol Biol , vol.353 , pp. 459-473
    • Yue, P.1    Li, Z.2    Moult, J.3
  • 14
    • 84857790275 scopus 로고    scopus 로고
    • Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs
    • A. David, R. Razali, M.N. Wass, and M.J.E. Sternberg Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs Hum Mutat 33 2012 359 363
    • (2012) Hum Mutat , vol.33 , pp. 359-363
    • David, A.1    Razali, R.2    Wass, M.N.3    Sternberg, M.J.E.4
  • 15
    • 84863010950 scopus 로고    scopus 로고
    • Three-dimensional reconstruction of protein networks provides insight into human genetic disease
    • X. Wang, X. Wei, B. Thijssen, J. Das, S.M. Lipkin, and H. Yu Three-dimensional reconstruction of protein networks provides insight into human genetic disease Nat Biotechnol 30 2012 159 164
    • (2012) Nat Biotechnol , vol.30 , pp. 159-164
    • Wang, X.1    Wei, X.2    Thijssen, B.3    Das, J.4    Lipkin, S.M.5    Yu, H.6
  • 16
    • 84885190937 scopus 로고    scopus 로고
    • The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions
    • C.M. Yates, and M.J.E. Sternberg The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions J Mol Biol 425 2013 3949 3963
    • (2013) J Mol Biol , vol.425 , pp. 3949-3963
    • Yates, C.M.1    Sternberg, M.J.E.2
  • 17
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: A case study using the Phyre server
    • L.A. Kelley, and M.J.E. Sternberg Protein structure prediction on the Web: a case study using the Phyre server Nat Protoc 4 2009 363 371
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 18
    • 84871614593 scopus 로고    scopus 로고
    • VariBench: A benchmark database for variations
    • P.S. Nair, and M. Vihinen VariBench: a benchmark database for variations Hum Mutat 34 2013 42 49
    • (2013) Hum Mutat , vol.34 , pp. 42-49
    • Nair, P.S.1    Vihinen, M.2
  • 20
    • 80053189298 scopus 로고    scopus 로고
    • Predicting the functional impact of protein mutations: Application to cancer genomics
    • B. Reva, Y. Antipin, and C. Sander Predicting the functional impact of protein mutations: application to cancer genomics Nucleic Acids Res 39 2011 e118
    • (2011) Nucleic Acids Res , vol.39 , pp. 118
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 21
    • 84871578629 scopus 로고    scopus 로고
    • Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models
    • H.A. Shihab, J. Gough, D.N. Cooper, P.D. Stenson, G.L.A. Barker, and K.J. Edwards et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models Hum Mutat 34 2013 57 65
    • (2013) Hum Mutat , vol.34 , pp. 57-65
    • Shihab, H.A.1    Gough, J.2    Cooper, D.N.3    Stenson, P.D.4    Barker, G.L.A.5    Edwards, K.J.6
  • 23
    • 17644384367 scopus 로고    scopus 로고
    • Minimum redundancy feature selection from microarray gene expression data
    • C. Ding, and H. Peng Minimum redundancy feature selection from microarray gene expression data J Bioinform Comput Biol 3 2005 185 205
    • (2005) J Bioinform Comput Biol , vol.3 , pp. 185-205
    • Ding, C.1    Peng, H.2
  • 25
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • J.A. Capra, and M. Singh Predicting functionally important residues from sequence conservation Bioinformatics 23 2007 1875 1882
    • (2007) Bioinformatics , vol.23 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 26
    • 79952764520 scopus 로고    scopus 로고
    • Performance of mutation pathogenicity prediction methods on missense variants
    • J. Thusberg, A. Olatubosun, and M. Vihinen Performance of mutation pathogenicity prediction methods on missense variants Hum Mutat 32 2011 358 368
    • (2011) Hum Mutat , vol.32 , pp. 358-368
    • Thusberg, J.1    Olatubosun, A.2    Vihinen, M.3
  • 27
    • 84865298225 scopus 로고    scopus 로고
    • FunSAV: Predicting the functional effect of single amino acid variants using a two-stage random forest model
    • M. Wang, X.-M. Zhao, K. Takemoto, H. Xu, Y. Li, and T. Akutsu et al. FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model PLoS One 7 2012 e43847
    • (2012) PLoS One , vol.7 , pp. 43847
    • Wang, M.1    Zhao, X.-M.2    Takemoto, K.3    Xu, H.4    Li, Y.5    Akutsu, T.6
  • 28
    • 0023710206 scopus 로고
    • Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach
    • E.R. DeLong, D.M. DeLong, and D.L. Clarke-Pearson Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach Biometrics 44 1988 837 845
    • (1988) Biometrics , vol.44 , pp. 837-845
    • Delong, E.R.1    Delong, D.M.2    Clarke-Pearson, D.L.3
  • 29
    • 84876239078 scopus 로고    scopus 로고
    • JSmol and the next-generation Web-based representation of 3D molecular structure as applied to proteopedia
    • R.M. Hanson, J. Prilusky, Z. Renjian, T. Nakane, and J.L. Sussman JSmol and the next-generation Web-based representation of 3D molecular structure as applied to proteopedia Isr J Chem 53 2013 207 216
    • (2013) Isr J Chem , vol.53 , pp. 207-216
    • Hanson, R.M.1    Prilusky, J.2    Renjian, Z.3    Nakane, T.4    Sussman, J.L.5
  • 30
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • P.C. Ng, and S. Henikoff Predicting deleterious amino acid substitutions Genome Res 11 2001 863 874
    • (2001) Genome Res , vol.11 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 31
    • 0035553153 scopus 로고    scopus 로고
    • HMLH1 and hMSH2 mutations in families with familial clustering of gastric cancer and hereditary non-polyposis colorectal cancer
    • J. Kim, H. Kim, S. Roh, K. Koo, D. Lee, and C. Yu et al. hMLH1 and hMSH2 mutations in families with familial clustering of gastric cancer and hereditary non-polyposis colorectal cancer Cancer Detect Prev 25 2001 503 510
    • (2001) Cancer Detect Prev , vol.25 , pp. 503-510
    • Kim, J.1    Kim, H.2    Roh, S.3    Koo, K.4    Lee, D.5    Yu, C.6
  • 34
    • 84876525081 scopus 로고    scopus 로고
    • Genome3D: A UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
    • T.E. Lewis, I. Sillitoe, A. Andreeva, T.L. Blundell, D.W.A. Buchan, and C. Chothia et al. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains Nucleic Acids Res 41 2013 D499 D507
    • (2013) Nucleic Acids Res , vol.41
    • Lewis, T.E.1    Sillitoe, I.2    Andreeva, A.3    Blundell, T.L.4    Buchan, D.W.A.5    Chothia, C.6
  • 36
    • 77958487982 scopus 로고    scopus 로고
    • Sequencing delivers diminishing returns for homology detection: Implications for mapping the protein universe
    • D. Chubb, B.R. Jefferys, M.J.E. Sternberg, and L.A. Kelley Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe Bioinformatics 26 2010 2664 2671
    • (2010) Bioinformatics , vol.26 , pp. 2664-2671
    • Chubb, D.1    Jefferys, B.R.2    Sternberg, M.J.E.3    Kelley, L.A.4
  • 37
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 38
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: An open source platform for ligand pocket detection
    • V. Le Guilloux, P. Schmidtke, and P. Tuffery Fpocket: an open source platform for ligand pocket detection BMC Bioinformatics 10 2009 168
    • (2009) BMC Bioinformatics , vol.10 , pp. 168
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 39
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • G. Csardi, and T. Nepusz The igraph software package for complex network research InterJ Complex Syst 1695 2006 1 9
    • (2006) InterJ Complex Syst , vol.1695 , pp. 1-9
    • Csardi, G.1    Nepusz, T.2
  • 40
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • C.T. Porter, G.J. Bartlett, and J.M. Thornton The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Res 32 2004 D129 D133
    • (2004) Nucleic Acids Res , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 41
    • 58149203230 scopus 로고    scopus 로고
    • PiSite: A database of protein interaction sites using multiple binding states in the PDB
    • M. Higurashi, T. Ishida, and K. Kinoshita PiSite: a database of protein interaction sites using multiple binding states in the PDB Nucleic Acids Res 37 2009 D360 D364
    • (2009) Nucleic Acids Res , vol.37
    • Higurashi, M.1    Ishida, T.2    Kinoshita, K.3
  • 42
    • 68949213019 scopus 로고    scopus 로고
    • A generic method for assignment of reliability scores applied to solvent accessibility predictions
    • B. Petersen, T.N. Petersen, P. Andersen, M. Nielsen, and C. Lundegaard A generic method for assignment of reliability scores applied to solvent accessibility predictions BMC Struct Biol 9 2009 51
    • (2009) BMC Struct Biol , vol.9 , pp. 51
    • Petersen, B.1    Petersen, T.N.2    Andersen, P.3    Nielsen, M.4    Lundegaard, C.5
  • 43
    • 14844342815 scopus 로고    scopus 로고
    • The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    • Z. Dosztányi, V. Csizmók, P. Tompa, and I. Simon The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins J Mol Biol 347 2005 827 839
    • (2005) J Mol Biol , vol.347 , pp. 827-839
    • Dosztányi, Z.1    Csizmók, V.2    Tompa, P.3    Simon, I.4
  • 44
    • 67049119327 scopus 로고    scopus 로고
    • Prediction of protein binding regions in disordered proteins
    • B. Meszaros, I. Simon, and Z. Dosztanyi Prediction of protein binding regions in disordered proteins PLoS Comput Biol 5 2009 e1000376
    • (2009) PLoS Comput Biol , vol.5 , pp. 1000376
    • Meszaros, B.1    Simon, I.2    Dosztanyi, Z.3
  • 45
    • 0019287872 scopus 로고
    • Thermostability and aliphatic index of globular proteins
    • A. Ikai Thermostability and aliphatic index of globular proteins J Biochem 88 1980 1895 1898
    • (1980) J Biochem , vol.88 , pp. 1895-1898
    • Ikai, A.1
  • 46
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • J. Kyte, and R.F. Doolittle A simple method for displaying the hydropathic character of a protein J Mol Biol 157 1982 105 132
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 47
    • 2442694043 scopus 로고    scopus 로고
    • Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms
    • R.J. Clifford, M.N. Edmonson, C. Nguyen, and K.H. Buetow Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms Bioinformatics 20 2004 1006 1014
    • (2004) Bioinformatics , vol.20 , pp. 1006-1014
    • Clifford, R.J.1    Edmonson, M.N.2    Nguyen, C.3    Buetow, K.H.4
  • 50
    • 80051787006 scopus 로고    scopus 로고
    • Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks
    • X. Xie, J. Jin, and Y. Mao Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks BMC Evol Biol 11 2011 242
    • (2011) BMC Evol Biol , vol.11 , pp. 242
    • Xie, X.1    Jin, J.2    Mao, Y.3
  • 51
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored
    • D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A. Roth, and P. Minguez et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored Nucleic Acids Res 39 2011 D561 D568
    • (2011) Nucleic Acids Res , vol.39
    • Szklarczyk, D.1    Franceschini, A.2    Kuhn, M.3    Simonovic, M.4    Roth, A.5    Minguez, P.6
  • 53
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • The UniProt Consortium
    • The UniProt Consortium Update on activities at the Universal Protein Resource (UniProt) in 2013 Nucleic Acids Res 41 2013 D43 D47
    • (2013) Nucleic Acids Res , vol.41
  • 54
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • S. Henikoff, and J.G. Henikoff Amino acid substitution matrices from protein blocks Proc Natl Acad Sci 89 1992 10915 10919
    • (1992) Proc Natl Acad Sci , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 58
    • 11244352554 scopus 로고    scopus 로고
    • Kernlab - An S4 package for kernel methods in R
    • A. Karatzoglou, and A. Smola kernlab - an S4 package for kernel methods in R J Stat Softw 11 2004 1 20
    • (2004) J Stat Softw , vol.11 , pp. 1-20
    • Karatzoglou, A.1    Smola, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.