메뉴 건너뛰기




Volumn 197, Issue 1, 2014, Pages 285-289

SNP2GO: Functional analysis of genome-wide association studies

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EVOLUTIONARY RATE; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOME; HAPLOTYPE; NONHUMAN; NOTE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TEMPERATURE ACCLIMATIZATION; ANIMAL; GENE ONTOLOGY; GENETICS; GENOMICS; HUMAN; PROCEDURES;

EID: 84901321219     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.160341     Document Type: Note
Times cited : (28)

References (36)
  • 1
    • 84972545970 scopus 로고
    • A survey of exact inference for contingency tables
    • Agresti, A., 1992 A survey of exact inference for contingency tables. Stat. Sci. 7: 131-153.
    • (1992) Stat. Sci. , vol.7 , pp. 131-153
    • Agresti, A.1
  • 2
    • 84889826091 scopus 로고    scopus 로고
    • Ontologies and functional genomics
    • in, edited by F. Azuaje and J. Dopazo. John Wiley & Sons, West Sussex, England
    • Al-Shahrour, F., and J. Dopazo, 2005 Ontologies and functional genomics, pp. 99-112 in Data Analysis and Visualization in Genomics and Proteomics, edited by F. Azuaje and J. Dopazo. John Wiley & Sons, West Sussex, England.
    • (2005) Data Analysis and Visualization in Genomics and Proteomics , pp. 99-112
    • Al-Shahrour, F.1    Dopazo, J.2
  • 4
    • 77953233453 scopus 로고    scopus 로고
    • Genome-wide association of 107 phenotypes in Arabidopsis thaliana inbred lines
    • Atwell, S., Y. S. Huang, B. J. Vilhjálmsson, G. Willems, M. Horton et al., 2010 Genome-wide association of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
    • (2010) Nature , vol.465 , pp. 627-631
    • Atwell, S.1    Huang, Y.S.2    Vilhjálmsson, B.J.3    Willems, G.4    Horton, M.5
  • 5
    • 84879673534 scopus 로고    scopus 로고
    • A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster
    • Bastide, H., A. Betancourt, V. Nolte, R. Tobler, P. Stöbe et al., 2013 A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genet. 9: e10003534.
    • (2013) PLoS Genet. , vol.9
    • Bastide, H.1    Betancourt, A.2    Nolte, V.3    Tobler, R.4    Stöbe, P.5
  • 6
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Y. Hochberg, 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289-300.
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 7
    • 58149253310 scopus 로고    scopus 로고
    • On the utility of gene set methods in genomewide association studies of quantitative traits
    • Chasman, D. I., 2008 On the utility of gene set methods in genomewide association studies of quantitative traits. Genet. Epidemiol. 32: 658-668.
    • (2008) Genet. Epidemiol. , vol.32 , pp. 658-668
    • Chasman, D.I.1
  • 8
    • 77953123145 scopus 로고    scopus 로고
    • Insights into colon cancer etiology via a regularized approach to gene set analysis of GWAS data
    • Chen, L. S., C. M. Hutter, J. D. Potter, Y. Yang, R. L. Prentice et al., 2010 Insights into colon cancer etiology via a regularized approach to gene set analysis of GWAS data. Am. J. Hum. Genet. 86: 860-871.
    • (2010) Am. J. Hum. Genet. , vol.86 , pp. 860-871
    • Chen, L.S.1    Hutter, C.M.2    Potter, J.D.3    Yang, Y.4    Prentice, R.L.5
  • 9
    • 44949198268 scopus 로고    scopus 로고
    • The impact of recombination on nucleotide substitutions in the human genome
    • Duret, L., and P. F. Arndt, 2008 The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet. 4: e1000071.
    • (2008) PLoS Genet. , vol.4
    • Duret, L.1    Arndt, P.F.2
  • 10
    • 84878020180 scopus 로고    scopus 로고
    • Meta-analysis methods for genome-wide association studies and beyond
    • Evangelou, E., and J. P. Ioannidis, 2013 Meta-analysis methods for genome-wide association studies and beyond. Nat. Rev. Genet. 14: 379-389.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 379-389
    • Evangelou, E.1    Ioannidis, J.P.2
  • 11
    • 37249060304 scopus 로고    scopus 로고
    • Positive selection near an inversion breakpoint on the neo-X chromosome of Drosophila americana
    • Evans, A. L., P. A. Mena, and B. F. McAllister, 2007 Positive selection near an inversion breakpoint on the neo-X chromosome of Drosophila americana. Genetics 177: 1303-1319.
    • (2007) Genetics , vol.177 , pp. 1303-1319
    • Evans, A.L.1    Mena, P.A.2    McAllister, B.F.3
  • 12
    • 0027183991 scopus 로고
    • Recombination and mammalian genome evolution
    • Eyre-Walker, A., 1993 Recombination and mammalian genome evolution. Proc. Biol. Sci. 252: 237-243.
    • (1993) Proc. Biol. Sci. , vol.252 , pp. 237-243
    • Eyre-Walker, A.1
  • 13
    • 84867096797 scopus 로고    scopus 로고
    • Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America
    • Fabian, D. K., M. Kapun, V. Nolte, R. Kofler, P. S. Schmidt et al., 2012 Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Mol. Ecol. 21: 4748-4769.
    • (2012) Mol. Ecol. , vol.21 , pp. 4748-4769
    • Fabian, D.K.1    Kapun, M.2    Nolte, V.3    Kofler, R.4    Schmidt, P.S.5
  • 14
    • 75149134369 scopus 로고    scopus 로고
    • A new permutation strategy of pathway-based approach for genomewide association study
    • Guo, Y., J. Li, Y. Chen, L. Zhang, and H. Deng, 2009 A new permutation strategy of pathway-based approach for genomewide association study. BMC Bioinformatics 10: 429.
    • (2009) BMC Bioinformatics , vol.10 , pp. 429
    • Guo, Y.1    Li, J.2    Chen, Y.3    Zhang, L.4    Deng, H.5
  • 15
    • 80053587873 scopus 로고    scopus 로고
    • Adaptation to climate across the Arabidopsis thaliana genome
    • Hancock, A. M., B. Brachi, N. Faure, M. W. Horton, L. B. Jarymowycz et al., 2011 Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86.
    • (2011) Science , vol.334 , pp. 83-86
    • Hancock, A.M.1    Brachi, B.2    Faure, N.3    Horton, M.W.4    Jarymowycz, L.B.5
  • 16
    • 77958486255 scopus 로고    scopus 로고
    • Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits
    • Holmans, P., 2010 Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits. Adv. Genet. 72: 141-179.
    • (2010) Adv. Genet. , vol.72 , pp. 141-179
    • Holmans, P.1
  • 17
    • 67649584052 scopus 로고    scopus 로고
    • Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder
    • Holmans, P., E. K. Green, J. S. Pahwa, M. A. Ferreira, S. M. Purcell et al., 2009 Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am. J. Hum. Genet. 85: 13-24.
    • (2009) Am. J. Hum. Genet. , vol.85 , pp. 13-24
    • Holmans, P.1    Green, E.K.2    Pahwa, J.S.3    Ferreira, M.A.4    Purcell, S.M.5
  • 18
    • 68949204302 scopus 로고    scopus 로고
    • Strategies and issues in the detection of pathway enrichment in genome-wide association studies
    • Hong, M. G., Y. Pawitan, P. K. Magnusson, and J. A. Prince, 2009 Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Hum. Genet. 126: 289-301.
    • (2009) Hum. Genet. , vol.126 , pp. 289-301
    • Hong, M.G.1    Pawitan, Y.2    Magnusson, P.K.3    Prince, J.A.4
  • 19
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • Hwang, D. G., and P. Green, 2004 Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc. Natl. Acad. Sci. USA 101: 13994-14001.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 20
    • 84859462157 scopus 로고    scopus 로고
    • The genomic basis of adaptive evolution in threespine sticklebacks
    • Jones, F. C., M. G. Grabherr, Y. F. Chan, P. Russell, E. Mauceli et al., 2012 The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55-61.
    • (2012) Nature , vol.484 , pp. 55-61
    • Jones, F.C.1    Grabherr, M.G.2    Chan, Y.F.3    Russell, P.4    Mauceli, E.5
  • 22
    • 84865123842 scopus 로고    scopus 로고
    • Gowinda: Unbiased analysis of gene set enrichment for genome-wide association studies
    • Kofler, R., and C. Schlötterer, 2012 Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies. Bioinformatics 28: 2084-2085.
    • (2012) Bioinformatics , vol.28 , pp. 2084-2085
    • Kofler, R.1    Schlötterer, C.2
  • 23
    • 77954300600 scopus 로고    scopus 로고
    • GSA-SNP: A general approach for gene set analysis of polymorphisms
    • Nam, D., J. Kim, S.-Y. Kim, and S. Kim, 2010 GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res. 38: W749-W754.
    • (2010) Nucleic Acids Res. , vol.38
    • Nam, D.1    Kim, J.2    Kim, S.-Y.3    Kim, S.4
  • 24
    • 67849101185 scopus 로고    scopus 로고
    • Gene set-based analysis of polymorphisms: Finding pathways or biological processes associated to traits in genome-wide association studies
    • Medina, I., D. Montaner, N. Bonifaci, M. A. Pujana, J. Carbonell et al., 2009 Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res. 37: W340-W344.
    • (2009) Nucleic Acids Res. , vol.37
    • Medina, I.1    Montaner, D.2    Bonifaci, N.3    Pujana, M.A.4    Carbonell, J.5
  • 25
    • 84874969184 scopus 로고    scopus 로고
    • PANTHER in 2013: Modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
    • Mi, H., A. Muruganujan, and P. D. Thomas, 2013 PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 41: D377-D386.
    • (2013) Nucleic Acids Res. , vol.41
    • Mi, H.1    Muruganujan, A.2    Thomas, P.D.3
  • 26
    • 84867574655 scopus 로고    scopus 로고
    • Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles
    • Orozco-terWengel, P., M. Kapun, V. Nolte, R. Kofler, T. Flatt et al., 2012 Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol. Ecol. 21: 4931-4941.
    • (2012) Mol. Ecol. , vol.21 , pp. 4931-4941
    • Orozco-terWengel, P.1    Kapun, M.2    Nolte, V.3    Kofler, R.4    Flatt, T.5
  • 27
    • 67651205715 scopus 로고    scopus 로고
    • Identifying relationships among genomic disease regions: Predicting genes at pathogenic SNP associations and rare deletions
    • International Schizophrenia Consortium
    • Raychaudhuri, S., R. M. Plenge, E. J. Rossin, A. C. Ng International Schizophrenia Consortium et al., 2009 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet. 5: e1000534.
    • (2009) PLoS Genet. , vol.5
    • Raychaudhuri, S.1    Plenge, R.M.2    Rossin, E.J.3    Ng, A.C.4
  • 28
    • 15544387147 scopus 로고    scopus 로고
    • Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster
    • Singh, N. D., P. F. Arndt, and D. A. Petrov, 2005 Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics 169: 709-722.
    • (2005) Genetics , vol.169 , pp. 709-722
    • Singh, N.D.1    Arndt, P.F.2    Petrov, D.A.3
  • 29
    • 35948989284 scopus 로고    scopus 로고
    • The OBO foundry: Coordinated evolution of ontologies to support biomedical data integration
    • Smith, B., M. Ashburner, C. Rosse, J. Bard, W. Bug et al., 2007 The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25: 1251-1255.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1251-1255
    • Smith, B.1    Ashburner, M.2    Rosse, C.3    Bard, J.4    Bug, W.5
  • 30
    • 43549095247 scopus 로고    scopus 로고
    • Sequence context affects the rate of short insertions and deletions in flies and primates
    • Tanay, A., and E. D. Siggia, 2008 Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol. 9: R37.
    • (2008) Genome Biol. , vol.9
    • Tanay, A.1    Siggia, E.D.2
  • 31
    • 84893147360 scopus 로고    scopus 로고
    • Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments
    • Tobler, R., S. U. Franssen, R. Kofler, P. Orozco-terWengel, V. Nolte et al., 2014 Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol. Biol. Evol. 31: 364-375.
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 364-375
    • Tobler, R.1    Franssen, S.U.2    Kofler, R.3    Orozco-terWengel, P.4    Nolte, V.5
  • 32
    • 84862564386 scopus 로고    scopus 로고
    • Investigating natural variation in Drosophila courtship song by the evolve and resequence approach
    • Turner, T. L., and P. M. Miller, 2012 Investigating natural variation in Drosophila courtship song by the evolve and resequence approach. Genetics 191: 633-642.
    • (2012) Genetics , vol.191 , pp. 633-642
    • Turner, T.L.1    Miller, P.M.2
  • 33
    • 79953735688 scopus 로고    scopus 로고
    • Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster
    • Turner, T. L., A. D. Steward, A. T. Fields, W. R. Rice, and A. M. Tarone, 2011 Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet. 7: e10001336.
    • (2011) PLoS Genet. , vol.7
    • Turner, T.L.1    Steward, A.D.2    Fields, A.T.3    Rice, W.R.4    Tarone, A.M.5
  • 34
    • 36249029788 scopus 로고    scopus 로고
    • Pathway-based approaches for analysis of genomewide association studies
    • Wang, K., M. Li, and M. Bucan, 2007 Pathway-based approaches for analysis of genomewide association studies. Am. J. Hum. Genet. 81: 1278-1283.
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 1278-1283
    • Wang, K.1    Li, M.2    Bucan, M.3
  • 35
    • 78549251736 scopus 로고    scopus 로고
    • Analysing biological pathways in genome-wide association studies
    • Wang, K., M. Li, and H. Hakonarson, 2012 Analysing biological pathways in genome-wide association studies. Nat. Rev. Genet. 11: 843-854.
    • (2012) Nat. Rev. Genet. , vol.11 , pp. 843-854
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 36
    • 77954246243 scopus 로고    scopus 로고
    • i-GSEA4GWAS: A web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study
    • Zhang, K., S. Cui, S. Chang, L. Zhang, and J. Wang, 2010 i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Res. 38: W90-W95.
    • (2010) Nucleic Acids Res. , vol.38
    • Zhang, K.1    Cui, S.2    Chang, S.3    Zhang, L.4    Wang, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.