메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

PaPI: Pseudo amino acid composition to score human protein-coding variants

Author keywords

Exome; Prediction; Pseudo amino acid composition; Sequencing; Variant

Indexed keywords

ALGORITHMS; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; CODES (SYMBOLS); FORECASTING; GENES; PROTEINS;

EID: 84928554654     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0554-8     Document Type: Article
Times cited : (49)

References (52)
  • 1
    • 79951475133 scopus 로고    scopus 로고
    • A decade's perspective on DNA sequencing technology
    • Mardis ER. A decade's perspective on DNA sequencing technology. Nature. 2011;470(7333):198-203.
    • (2011) Nature , vol.470 , Issue.7333 , pp. 198-203
    • Mardis, E.R.1
  • 2
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11(1):31-46.
    • (2010) Nat Rev Genet , vol.11 , Issue.1 , pp. 31-46
    • Metzker, M.L.1
  • 3
    • 84863529201 scopus 로고    scopus 로고
    • Weighted pooling-practical and cost-effective techniques for pooled high-throughput sequencing
    • Golan D, Erlich Y, Rosset S. Weighted pooling-practical and cost-effective techniques for pooled high-throughput sequencing. Bioinformatics. 2012;28(12):i197-206.
    • (2012) Bioinformatics , vol.28 , Issue.12 , pp. i197-206
    • Golan, D.1    Erlich, Y.2    Rosset, S.3
  • 6
    • 79953176952 scopus 로고    scopus 로고
    • Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia
    • Yan XJ, Xu J, Gu ZH, Pan CM, Lu G, Shen Y, et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet. 2011;43(4):309-15.
    • (2011) Nat Genet , vol.43 , Issue.4 , pp. 309-315
    • Yan, X.J.1    Xu, J.2    Gu, Z.H.3    Pan, C.M.4    Lu, G.5    Shen, Y.6
  • 7
    • 84893720400 scopus 로고    scopus 로고
    • Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol
    • Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang ZZ, et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet. 2014;94(2):233-45.
    • (2014) Am J Hum Genet , vol.94 , Issue.2 , pp. 233-245
    • Lange, L.A.1    Hu, Y.2    Zhang, H.3    Xue, C.4    Schmidt, E.M.5    Tang, Z.Z.6
  • 10
    • 84863556835 scopus 로고    scopus 로고
    • Evolution and functional impact of rare coding variation from deep sequencing of human exomes
    • Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012;337(6090):64-9.
    • (2012) Science , vol.337 , Issue.6090 , pp. 64-69
    • Tennessen, J.A.1    Bigham, A.W.2    O'Connor, T.D.3    Fu, W.4    Kenny, E.E.5    Gravel, S.6
  • 11
    • 84891809093 scopus 로고    scopus 로고
    • ClinVar: public archive of relationships among sequence variation and human phenotype
    • Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(Database issue):D980-985.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. D980-985
    • Landrum, M.J.1    Lee, J.M.2    Riley, G.R.3    Jang, W.4    Rubinstein, W.S.5    Church, D.M.6
  • 13
    • 84864616473 scopus 로고    scopus 로고
    • Human genomic disease variants: a neutral evolutionary explanation
    • Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, et al. Human genomic disease variants: a neutral evolutionary explanation. Genome Res. 2012;22(8):1383-94.
    • (2012) Genome Res , vol.22 , Issue.8 , pp. 1383-1394
    • Dudley, J.T.1    Kim, Y.2    Liu, L.3    Markov, G.J.4    Gerold, K.5    Chen, R.6
  • 14
    • 80053189298 scopus 로고    scopus 로고
    • Predicting the functional impact of protein mutations: application to cancer genomics
    • Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39(17):e118.
    • (2011) Nucleic Acids Res , vol.39 , Issue.17
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 15
    • 84871578629 scopus 로고    scopus 로고
    • Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models
    • Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2013;34(1):57-65.
    • (2013) Hum Mutat , vol.34 , Issue.1 , pp. 57-65
    • Shihab, H.A.1    Gough, J.2    Cooper, D.N.3    Stenson, P.D.4    Barker, G.L.5    Edwards, K.J.6
  • 16
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-81.
    • (2009) Nat Protoc , vol.4 , Issue.7 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 18
    • 78651237647 scopus 로고    scopus 로고
    • Identifying a high fraction of the human genome to be under selective constraint using GERP++
    • Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010;6(12):e1001025.
    • (2010) PLoS Comput Biol , vol.6 , Issue.12 , pp. e1001025
    • Davydov, E.V.1    Goode, D.L.2    Sirota, M.3    Cooper, G.M.4    Sidow, A.5    Batzoglou, S.6
  • 19
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010;20(1):110-21.
    • (2010) Genome Res , vol.20 , Issue.1 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 20
    • 66349086264 scopus 로고    scopus 로고
    • Identifying novel constrained elements by exploiting biased substitution patterns
    • Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics. 2009;25(12):i54-62.
    • (2009) Bioinformatics , vol.25 , Issue.12 , pp. i54-62
    • Garber, M.1    Guttman, M.2    Clamp, M.3    Zody, M.C.4    Friedman, N.5    Xie, X.6
  • 21
    • 69749122314 scopus 로고    scopus 로고
    • Identification of deleterious mutations within three human genomes
    • Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Res. 2009;19(9):1553-61.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1553-1561
    • Chun, S.1    Fay, J.C.2
  • 22
    • 84890056814 scopus 로고    scopus 로고
    • Feature-based classification of amino acid substitutions outside conserved functional protein domains
    • Gemovic B, Perovic V, Glisic S, Veljkovic N. Feature-based classification of amino acid substitutions outside conserved functional protein domains. Sci World J. 2013;2013:948617.
    • (2013) Sci World J , vol.2013 , pp. 948617
    • Gemovic, B.1    Perovic, V.2    Glisic, S.3    Veljkovic, N.4
  • 24
    • 84896118646 scopus 로고    scopus 로고
    • Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge
    • Kassahn KS, Scott HS, Caramins MC. Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge. Hum Mutat. 2014;35(4):413-23.
    • (2014) Hum Mutat , vol.35 , Issue.4 , pp. 413-423
    • Kassahn, K.S.1    Scott, H.S.2    Caramins, M.C.3
  • 25
    • 84886261399 scopus 로고    scopus 로고
    • Predicting the functional consequences of non-synonymous DNA sequence variants-evaluation of bioinformatics tools and development of a consensus strategy
    • Frousios K, Iliopoulos CS, Schlitt T, Simpson MA. Predicting the functional consequences of non-synonymous DNA sequence variants-evaluation of bioinformatics tools and development of a consensus strategy. Genomics. 2013;102(4):223-8.
    • (2013) Genomics , vol.102 , Issue.4 , pp. 223-228
    • Frousios, K.1    Iliopoulos, C.S.2    Schlitt, T.3    Simpson, M.A.4
  • 26
    • 79953715693 scopus 로고    scopus 로고
    • Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, condel
    • Gonzalez-Perez A, Lopez-Bigas N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, condel. Am J Hum Genet. 2011;88(4):440-9.
    • (2011) Am J Hum Genet , vol.88 , Issue.4 , pp. 440-449
    • Gonzalez-Perez, A.1    Lopez-Bigas, N.2
  • 29
    • 84898743768 scopus 로고    scopus 로고
    • Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families
    • Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, et al. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet. 2014;94(4):599-610.
    • (2014) Am J Hum Genet , vol.94 , Issue.4 , pp. 599-610
    • Singleton, M.V.1    Guthery, S.L.2    Voelkerding, K.V.3    Chen, K.4    Kennedy, B.5    Margraf, R.L.6
  • 30
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein cellular attributes using pseudo-amino acid composition
    • Chou KC. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins. 2001;43(3):246-55.
    • (2001) Proteins , vol.43 , Issue.3 , pp. 246-255
    • Chou, K.C.1
  • 31
    • 12744279642 scopus 로고    scopus 로고
    • Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    • Chou KC. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics. 2005;21(1):10-9.
    • (2005) Bioinformatics , vol.21 , Issue.1 , pp. 10-19
    • Chou, K.C.1
  • 32
    • 77950471248 scopus 로고    scopus 로고
    • Identification of ATP binding residues of a protein from its primary sequence
    • Chauhan JS, Mishra NK, Raghava GP. Identification of ATP binding residues of a protein from its primary sequence. BMC Bioinformatics. 2009;10:434.
    • (2009) BMC Bioinformatics. , vol.10 , pp. 434
    • Chauhan, J.S.1    Mishra, N.K.2    Raghava, G.P.3
  • 33
    • 84888219181 scopus 로고    scopus 로고
    • Exploring the composition of protein-ligand binding sites on a large scale
    • Khazanov NA, Carlson HA. Exploring the composition of protein-ligand binding sites on a large scale. PLoS Comput Biol. 2013;9(11):e1003321.
    • (2013) PLoS Comput Biol , vol.9 , Issue.11 , pp. e1003321
    • Khazanov, N.A.1    Carlson, H.A.2
  • 34
    • 79957599007 scopus 로고    scopus 로고
    • Markov models of amino acid substitution to study proteins with intrinsically disordered regions
    • Szalkowski AM, Anisimova M. Markov models of amino acid substitution to study proteins with intrinsically disordered regions. PLoS One. 2011;6(5):e20488.
    • (2011) PLoS One , vol.6 , Issue.5 , pp. e20488
    • Szalkowski, A.M.1    Anisimova, M.2
  • 35
    • 84892739749 scopus 로고    scopus 로고
    • Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset
    • de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM. Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. PLoS Comput Biol. 2013;9(12):e1003382.
    • (2013) PLoS Comput Biol , vol.9 , Issue.12 , pp. e1003382
    • Beer, T.A.1    Laskowski, R.A.2    Parks, S.L.3    Sipos, B.4    Goldman, N.5    Thornton, J.M.6
  • 36
    • 34848835086 scopus 로고    scopus 로고
    • Spectrum of disease-causing mutations in protein secondary structures
    • Khan S, Vihinen M. Spectrum of disease-causing mutations in protein secondary structures. BMC Struct Biol. 2007;7:56.
    • (2007) BMC Struct Biol. , vol.7 , pp. 56
    • Khan, S.1    Vihinen, M.2
  • 37
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Mach Learn. 2001;45:27.
    • (2001) Mach Learn. , vol.45 , pp. 27
    • Breiman, L.1
  • 38
    • 84861730860 scopus 로고    scopus 로고
    • Random forests for genomic data analysis
    • Chen X, Ishwaran H. Random forests for genomic data analysis. Genomics. 2012;99(6):323-9.
    • (2012) Genomics , vol.99 , Issue.6 , pp. 323-329
    • Chen, X.1    Ishwaran, H.2
  • 39
    • 84867301515 scopus 로고    scopus 로고
    • Predicting the functional effect of amino acid substitutions and indels
    • Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS One. 2012;7(10):e46688.
    • (2012) PLoS One , vol.7 , Issue.10 , pp. e46688
    • Choi, Y.1    Sims, G.E.2    Murphy, S.3    Miller, J.R.4    Chan, A.P.5
  • 40
    • 84860715301 scopus 로고    scopus 로고
    • Meconium ileus caused by mutations in GUCY2C, encoding the CFTR-activating guanylate cyclase 2C
    • Romi H, Cohen I, Landau D, Alkrinawi S, Yerushalmi B, Hershkovitz R, et al. Meconium ileus caused by mutations in GUCY2C, encoding the CFTR-activating guanylate cyclase 2C. Am J Hum Genet. 2012;90(5):893-9.
    • (2012) Am J Hum Genet , vol.90 , Issue.5 , pp. 893-899
    • Romi, H.1    Cohen, I.2    Landau, D.3    Alkrinawi, S.4    Yerushalmi, B.5    Hershkovitz, R.6
  • 41
    • 14744268993 scopus 로고    scopus 로고
    • Recognition and signal transduction mechanism of Escherichia coli heat-stable enterotoxin and its receptor, guanylate cyclase C
    • Hasegawa M, Shimonishi Y. Recognition and signal transduction mechanism of Escherichia coli heat-stable enterotoxin and its receptor, guanylate cyclase C. J Peptide Res Off J Am Peptide Soc. 2005;65(2):261-71.
    • (2005) J Peptide Res Off J Am Peptide Soc , vol.65 , Issue.2 , pp. 261-271
    • Hasegawa, M.1    Shimonishi, Y.2
  • 42
    • 84858602406 scopus 로고    scopus 로고
    • InterPro in 2011: new developments in the family and domain prediction database
    • Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012;40(Database issue):D306-312.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE , pp. D306-312
    • Hunter, S.1    Jones, P.2    Mitchell, A.3    Apweiler, R.4    Attwood, T.K.5    Bateman, A.6
  • 43
    • 7044237350 scopus 로고    scopus 로고
    • In silico prediction of the deleterious effect of a mutation: proceed with caution in clinical genetics
    • Tchernitchko D, Goossens M, Wajcman H. In silico prediction of the deleterious effect of a mutation: proceed with caution in clinical genetics. Clin Chem. 2004;50(11):1974-8.
    • (2004) Clin Chem , vol.50 , Issue.11 , pp. 1974-1978
    • Tchernitchko, D.1    Goossens, M.2    Wajcman, H.3
  • 44
    • 79952764520 scopus 로고    scopus 로고
    • Performance of mutation pathogenicity prediction methods on missense variants
    • Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat. 2011;32(4):358-68.
    • (2011) Hum Mutat , vol.32 , Issue.4 , pp. 358-368
    • Thusberg, J.1    Olatubosun, A.2    Vihinen, M.3
  • 45
    • 84904410108 scopus 로고    scopus 로고
    • Majority vote and other problems when using computational tools
    • Vihinen M. Majority vote and other problems when using computational tools. Hum Mutat. 2014;35(8):912-4.
    • (2014) Hum Mutat , vol.35 , Issue.8 , pp. 912-914
    • Vihinen, M.1
  • 46
    • 0030955263 scopus 로고    scopus 로고
    • Understanding the recognition of protein structural classes by amino acid composition
    • Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins. 1997;29(2):172-85.
    • (1997) Proteins , vol.29 , Issue.2 , pp. 172-185
    • Bahar, I.1    Atilgan, A.R.2    Jernigan, R.L.3    Erman, B.4
  • 47
    • 0037233515 scopus 로고    scopus 로고
    • Subcellular location prediction of apoptosis proteins
    • Zhou GP, Doctor K. Subcellular location prediction of apoptosis proteins. Proteins. 2003;50(1):44-8.
    • (2003) Proteins , vol.50 , Issue.1 , pp. 44-48
    • Zhou, G.P.1    Doctor, K.2
  • 48
    • 84859932176 scopus 로고    scopus 로고
    • PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions
    • Du P, Wang X, Xu C, Gao Y. PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. Anal Biochem. 2012;425(2):117-9.
    • (2012) Anal Biochem , vol.425 , Issue.2 , pp. 117-119
    • Du, P.1    Wang, X.2    Xu, C.3    Gao, Y.4
  • 49
    • 52249101769 scopus 로고    scopus 로고
    • Short linear motifs recognized by SH2, SH3 and Ser/Thr kinase domains are conserved in disordered protein regions
    • Ren S, Uversky VN, Chen Z, Dunker AK, Obradovic Z. Short linear motifs recognized by SH2, SH3 and Ser/Thr kinase domains are conserved in disordered protein regions. BMC Genomics. 2008;9 Suppl 2:S26.
    • (2008) BMC Genomics , vol.9 , pp. S26
    • Ren, S.1    Uversky, V.N.2    Chen, Z.3    Dunker, A.K.4    Obradovic, Z.5
  • 50
    • 84888024210 scopus 로고    scopus 로고
    • Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution
    • Koel BF, Burke DF, Bestebroer TM, van der Vliet S, Zondag GC, Vervaet G, et al. Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution. Science. 2013;342(6161):976-9.
    • (2013) Science , vol.342 , Issue.6161 , pp. 976-979
    • Koel, B.F.1    Burke, D.F.2    Bestebroer, T.M.3    Vliet, S.4    Zondag, G.C.5    Vervaet, G.6
  • 52
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
    • (2010) Nucleic Acids Res , vol.38 , Issue.16 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.