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Volumn 27, Issue 13, 2011, Pages i561-i567

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms

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EID: 84983120924     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq384     Document Type: Conference Paper
Times cited : (6)

References (57)
  • 1
    • 25444482801 scopus 로고    scopus 로고
    • Speeding disease gene discovery by sequence based candidate prioritization
    • Adie, E.A. et al. (2005) Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics, 6, 55.
    • (2005) BMC Bioinformatics , vol.6 , pp. 55
    • Adie, E.A.1
  • 2
    • 33645104470 scopus 로고    scopus 로고
    • SUSPECTS: Enabling fast and effective prioritization of positional candidates
    • Adie, E.A. et al. (2006) SUSPECTS: Enabling fast and effective prioritization of positional candidates. Bioinformatics, 22, 773-774.
    • (2006) Bioinformatics , vol.22 , pp. 773-774
    • Adie, E.A.1
  • 3
    • 33646568805 scopus 로고    scopus 로고
    • Gene prioritization through genomic data fusion
    • Aerts, S. et al. (2006) Gene prioritization through genomic data fusion. Nat. Biotechnol., 24, 537-544.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 537-544
    • Aerts, S.1
  • 4
    • 41849139980 scopus 로고    scopus 로고
    • Prediction of human disease genes by human-mouse conserved coexpression analysis
    • Ala, U. et al. (2008) Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput. Biol., 4, e1000043.
    • (2008) PLoS Comput. Biol. , vol.4 , pp. e1000043
    • Ala, U.1
  • 5
    • 55449120805 scopus 로고    scopus 로고
    • Genetic mapping in human disease
    • Altshuler, D. et al. (2008) Genetic mapping in human disease. Science, 322, 881-888.
    • (2008) Science , vol.322 , pp. 881-888
    • Altshuler, D.1
  • 6
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M. et al. (2000) Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 7
    • 38549122308 scopus 로고    scopus 로고
    • InParanoid 6: Eukaryotic ortholog clusters with inparalogs
    • Berglund, A.C. et al. (2008) InParanoid 6: Eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res., 36, D263-D266.
    • (2008) Nucleic Acids Res. , vol.36 , pp. D263-D266
    • Berglund, A.C.1
  • 8
    • 58149197592 scopus 로고    scopus 로고
    • The Mouse Genome Database genotypes::phenotypes
    • Blake, J.A. et al. (2009) The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res., 37, D712-D719.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D712-D719
    • Blake, J.A.1
  • 9
    • 33846073818 scopus 로고    scopus 로고
    • MINT: The Molecular INTeraction database
    • Chatr-Aryamontri, A. et al. (2007) MINT: The Molecular INTeraction database. Nucleic Acids Res., 35, D572-D574.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D572-D574
    • Chatr-Aryamontri, A.1
  • 10
    • 38049136610 scopus 로고    scopus 로고
    • Improved human disease candidate gene prioritization using mouse phenotype
    • Chen, J. et al. (2007) Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics, 8, 392.
    • (2007) BMC Bioinformatics , vol.8 , pp. 392
    • Chen, J.1
  • 11
    • 73249152476 scopus 로고    scopus 로고
    • Disease candidate gene identification and prioritization using protein interaction networks
    • Chen, J. et al. (2009) Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics, 10, 73.
    • (2009) BMC Bioinformatics , vol.10 , pp. 73
    • Chen, J.1
  • 12
    • 44349124113 scopus 로고    scopus 로고
    • The genetics and immunopathogenesis of inflammatory bowel disease
    • Cho, J.H. (2008) The genetics and immunopathogenesis of inflammatory bowel disease. Nat. Rev. Immunol., 8, 458-466.
    • (2008) Nat. Rev. Immunol. , vol.8 , pp. 458-466
    • Cho, J.H.1
  • 13
    • 25144501575 scopus 로고    scopus 로고
    • Genetic association studies
    • Cordell, H.J. and Clayton, D.G. (2005) Genetic association studies. Lancet, 366, 1121-1131.
    • (2005) Lancet , vol.366 , pp. 1121-1131
    • Cordell, H.J.1    Clayton, D.G.2
  • 14
    • 41949118715 scopus 로고    scopus 로고
    • Network properties of genes harboring inherited disease mutations
    • Feldman, I. et al. (2008) Network properties of genes harboring inherited disease mutations. Proc. Natl Acad. Sci. USA, 105, 4323-4328.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 4323-4328
    • Feldman, I.1
  • 15
    • 33646884801 scopus 로고    scopus 로고
    • Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
    • Franke, L. et al. (2006) Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet., 78, 1011-1025.
    • (2006) Am. J. Hum. Genet. , vol.78 , pp. 1011-1025
    • Franke, L.1
  • 16
    • 0037580196 scopus 로고    scopus 로고
    • A similarity-based method for genomewide prediction of disease-relevant human genes
    • Freudenberg, J. and Propping, P. (2002) A similarity-based method for genomewide prediction of disease-relevant human genes. Bioinformatics, 18 (Suppl. 2), S110-S115.
    • (2002) Bioinformatics , vol.18 , pp. S110-S115
    • Freudenberg, J.1    Propping, P.2
  • 17
    • 58549096683 scopus 로고    scopus 로고
    • Decanalization and the origin of complex disease
    • Gibson, G. (2009) Decanalization and the origin of complex disease. Nat. Rev. Genet., 10, 134-140.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 134-140
    • Gibson, G.1
  • 18
    • 34547140875 scopus 로고    scopus 로고
    • The human disease network
    • Goh, K.I. et al. (2007) The human disease network. Proc. Natl Acad. Sci. USA, 104, 8685-8690.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 8685-8690
    • Goh, K.I.1
  • 19
  • 20
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker, T. and Sharan, R. (2008) Protein networks in disease. Genome Res., 18, 644-652.
    • (2008) Genome Res. , vol.18 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 21
    • 0035865078 scopus 로고    scopus 로고
    • Human disease genes
    • Jimenez-Sanchez, G. et al. (2001) Human disease genes. Nature, 409, 853-855.
    • (2001) Nature , vol.409 , pp. 853-855
    • Jimenez-Sanchez, G.1
  • 22
    • 36349010138 scopus 로고    scopus 로고
    • Protein interactions and disease: Computational approaches to uncover the etiology of diseases
    • Kann, M.G. (2007) Protein interactions and disease: Computational approaches to uncover the etiology of diseases. Brief. Bioinform., 8, 333-346.
    • (2007) Brief. Bioinform. , vol.8 , pp. 333-346
    • Kann, M.G.1
  • 23
    • 77950351474 scopus 로고    scopus 로고
    • Advances in translational bioinformatics: Computational approaches for the hunting of disease genes
    • Kann, M.G. (2010) Advances in translational bioinformatics: Computational approaches for the hunting of disease genes. Brief. Bioinform., 11, 96-110.
    • (2010) Brief. Bioinform. , vol.11 , pp. 96-110
    • Kann, M.G.1
  • 24
    • 0038817774 scopus 로고    scopus 로고
    • EVOC: A controlled vocabulary for unifying gene expression data
    • Kelso, J. et al. (2003) eVOC: A controlled vocabulary for unifying gene expression data. Genome Res., 13, 1222-1230.
    • (2003) Genome Res. , vol.13 , pp. 1222-1230
    • Kelso, J.1
  • 25
    • 33846047770 scopus 로고    scopus 로고
    • IntAct-open source resource for molecular interaction data
    • Kerrien, S. et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res., 35, D561-D565.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D561-D565
    • Kerrien, S.1
  • 26
    • 33947095027 scopus 로고    scopus 로고
    • A human phenome-interactome network of protein complexes implicated in genetic disorders
    • Lage, K. et al. (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat. Biotechnol., 25, 309-316.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 309-316
    • Lage, K.1
  • 27
    • 48249158278 scopus 로고    scopus 로고
    • The implications of human metabolic network topology for disease comorbidity
    • Lee, D.S. et al. (2008) The implications of human metabolic network topology for disease comorbidity. Proc. Natl Acad. Sci. USA, 105, 9880-9885.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 9880-9885
    • Lee, D.S.1
  • 28
    • 33748856594 scopus 로고    scopus 로고
    • An information-theoretic definition of similarity
    • In: Shavlik, J.W. (ed.) Madison, WI, USA. Morgan Kaufmann Publishers, San Francisco, CA, USA
    • Lin, D. (1998) An information-theoretic definition of similarity. In: Shavlik, J.W. (ed.) Proceedings of the 15th International Conference on Machine Learning (ICML- 98). Madison, WI, USA. Morgan Kaufmann Publishers, San Francisco, CA, USA, pp. 296-304.
    • (1998) Proceedings of the 15th International Conference on Machine Learning (ICML- 98) , pp. 296-304
    • Lin, D.1
  • 29
    • 0028230073 scopus 로고
    • Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches
    • Lowe, H.J. and Barnett, G.O. (1994) Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches. JAMA, 271, 1103-1108.
    • (1994) JAMA , vol.271 , pp. 1103-1108
    • Lowe, H.J.1    Barnett, G.O.2
  • 30
    • 77951952127 scopus 로고    scopus 로고
    • The power of protein interaction networks for associating genes with diseases
    • Navlakha, S. and Kingsford, C. (2010) The power of protein interaction networks for associating genes with diseases. Bioinformatics, 26, 1057-1063.
    • (2010) Bioinformatics , vol.26 , pp. 1057-1063
    • Navlakha, S.1    Kingsford, C.2
  • 31
    • 33645127443 scopus 로고    scopus 로고
    • Genetic medicines: Treatment strategies for hereditary disorders
    • O'Connor, T.P. and Crystal, R.G. (2006) Genetic medicines: Treatment strategies for hereditary disorders. Nat. Rev. Genet., 7, 261-276.
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 261-276
    • O'Connor, T.P.1    Crystal, R.G.2
  • 32
    • 59649111554 scopus 로고    scopus 로고
    • Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: Case study of primary immunodeficiencies
    • Ortutay, C. and Vihinen, M. (2009) Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: Case study of primary immunodeficiencies. Nucleic Acids Res., 37, 622-628.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 622-628
    • Ortutay, C.1    Vihinen, M.2
  • 33
    • 33845545435 scopus 로고    scopus 로고
    • The modular nature of genetic diseases
    • Oti, M. and Brunner, H.G. (2007) The modular nature of genetic diseases. Clin. Genet., 71, 1-11.
    • (2007) Clin. Genet. , vol.71 , pp. 1-11
    • Oti, M.1    Brunner, H.G.2
  • 34
    • 46249127253 scopus 로고    scopus 로고
    • Identifying gene-disease associations using centrality on a literature mined gene-interaction network
    • Ozgür, A. et al. (2008) Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics, 24, i277-i285.
    • (2008) Bioinformatics , vol.24 , pp. i277-i285
    • Ozgür, A.1
  • 35
    • 0036649742 scopus 로고    scopus 로고
    • Association of genes to genetically inherited diseases using data mining
    • Perez-Iratxeta, C. et al. (2002) Association of genes to genetically inherited diseases using data mining. Nat. Genet., 31, 316-319.
    • (2002) Nat. Genet. , vol.31 , pp. 316-319
    • Perez-Iratxeta, C.1
  • 36
    • 34547601280 scopus 로고    scopus 로고
    • Update of the G2D tool for prioritization of gene candidates to inherited diseases
    • Perez-Iratxeta, C. et al. (2007) Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic Acids Res., 35, W212-W216.
    • (2007) Nucleic Acids Res. , vol.35 , pp. W212-W216
    • Perez-Iratxeta, C.1
  • 37
    • 58149193222 scopus 로고    scopus 로고
    • Human Protein Reference Database-2009 update
    • Prasad, T.S.K. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D767-D772
    • Prasad, T.S.K.1
  • 38
    • 68249085263 scopus 로고    scopus 로고
    • The Gene Ontology's Reference Genome Project: A unified framework for functional annotation across species
    • Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: A unified framework for functional annotation across species. PLoS Comput. Biol., 5, e1000431.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000431
  • 39
    • 84954358609 scopus 로고    scopus 로고
    • The Human Phenotype Ontology: A tool for annotating and analyzing human hereditary disease
    • Robinson, P.N. et al. (2008) The Human Phenotype Ontology: A tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet., 83, 610-615.
    • (2008) Am. J. Hum. Genet. , vol.83 , pp. 610-615
    • Robinson, P.N.1
  • 40
    • 38549163153 scopus 로고    scopus 로고
    • CORUM: The comprehensive resource of mammalian protein complexes
    • Ruepp, A. et al. (2008) CORUM: The comprehensive resource of mammalian protein complexes. Nucleic Acids Res., 36, D646-D650.
    • (2008) Nucleic Acids Res. , vol.36 , pp. D646-D650
    • Ruepp, A.1
  • 41
    • 0347755535 scopus 로고    scopus 로고
    • The database of interacting proteins: 2004 update
    • Salwinski, L. et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D449-D451
    • Salwinski, L.1
  • 42
    • 34250201123 scopus 로고    scopus 로고
    • GOTax: Investigating biological processes and biochemical activities along the taxonomic tree
    • Schlicker, A. et al. (2007) GOTax: Investigating biological processes and biochemical activities along the taxonomic tree. Genome Biol., 8, R33.
    • (2007) Genome Biol. , vol.8 , pp. R33
    • Schlicker, A.1
  • 43
    • 75549086209 scopus 로고    scopus 로고
    • FunSimMat update: New features for exploring functional similarity
    • Schlicker, A. and Albrecht, M. (2010) FunSimMat update: New features for exploring functional similarity. Nucleic Acids Res., 38, D244-D248.
    • (2010) Nucleic Acids Res. , vol.38 , pp. D244-D248
    • Schlicker, A.1    Albrecht, M.2
  • 44
    • 17744373329 scopus 로고    scopus 로고
    • Genetics of Crohn disease, an archetypal inflammatory barrier disease
    • Schreiber, S. et al. (2005) Genetics of Crohn disease, an archetypal inflammatory barrier disease. Nat. Rev. Genet., 6, 376-388.
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 376-388
    • Schreiber, S.1
  • 45
    • 40249113345 scopus 로고    scopus 로고
    • Commonality of functional annotation: A method for prioritization of candidate genes from genome-wide linkage studies
    • Shriner, D. et al. (2008) Commonality of functional annotation: A method for prioritization of candidate genes from genome-wide linkage studies. Nucleic Acids Res., 36, e26.
    • (2008) Nucleic Acids Res. , vol.36 , pp. e26
    • Shriner, D.1
  • 46
    • 26844450908 scopus 로고    scopus 로고
    • The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
    • Smith, C.L. et al. (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol., 6, R7.
    • (2005) Genome Biol. , vol.6 , pp. R7
    • Smith, C.L.1
  • 47
    • 24944561852 scopus 로고    scopus 로고
    • Genetic linkage studies
    • Teare, M.D. and Barrett, J.H. (2005) Genetic linkage studies. Lancet, 366, 1036-1044.
    • (2005) Lancet , vol.366 , pp. 1036-1044
    • Teare, M.D.1    Barrett, J.H.2
  • 48
    • 15044341082 scopus 로고    scopus 로고
    • Integration of text- And data-mining using ontologies successfully selects disease gene candidates
    • Tiffin, N. et al. (2005) Integration of text- And data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res., 33, 1544-1552.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 1544-1552
    • Tiffin, N.1
  • 49
    • 77956519624 scopus 로고    scopus 로고
    • A guide to web tools to prioritize candidate genes
    • in press
    • Tranchevent, L.C. et al. (2010) A guide to web tools to prioritize candidate genes. Brief. Bioinform., in press.
    • (2010) Brief. Bioinform.
    • Tranchevent, L.C.1
  • 50
    • 1542787787 scopus 로고    scopus 로고
    • POCUS: Mining genomic sequence annotation to predict disease genes
    • Turner, F.S. et al. (2003) POCUS: Mining genomic sequence annotation to predict disease genes. Genome Biol., 4, R75.
    • (2003) Genome Biol. , vol.4 , pp. R75
    • Turner, F.S.1
  • 51
    • 58149191270 scopus 로고    scopus 로고
    • The universal protein resource (UniProt) 2009
    • UniProt Consortium (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D169-D174
  • 52
    • 33646058032 scopus 로고    scopus 로고
    • A text-mining analysis of the human phenome
    • van Driel, M.A. et al. (2006) A text-mining analysis of the human phenome. Eur. J. Hum. Genet., 14, 535-542.
    • (2006) Eur. J. Hum. Genet. , vol.14 , pp. 535-542
    • Van Driel, M.A.1
  • 53
    • 33746326504 scopus 로고    scopus 로고
    • Bioinformatics methods for identifying candidate disease genes
    • van Driel, M.A. and Brunner, H.G. (2006) Bioinformatics methods for identifying candidate disease genes. Hum. Genomics, 2, 429-432.
    • (2006) Hum. Genomics , vol.2 , pp. 429-432
    • Van Driel, M.A.1    Brunner, H.G.2
  • 54
    • 13444288174 scopus 로고    scopus 로고
    • E-MSD: An integrated data resource for bioinformatics
    • Velankar, S. et al. (2005) E-MSD: An integrated data resource for bioinformatics. Nucleic Acids Res., 33, D262-D265.
    • (2005) Nucleic Acids Res. , vol.33 , pp. D262-D265
    • Velankar, S.1
  • 55
    • 43249114206 scopus 로고    scopus 로고
    • Network-based global inference of human disease genes
    • Wu, X. et al. (2008) Network-based global inference of human disease genes. Mol. Syst. Biol., 4, 189.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 189
    • Wu, X.1
  • 56
    • 58349100277 scopus 로고    scopus 로고
    • Gene-disease relationship discovery based on model-driven data integration and database view definition
    • Yilmaz, S. et al. (2009) Gene-disease relationship discovery based on model-driven data integration and database view definition. Bioinformatics, 25, 230-236.
    • (2009) Bioinformatics , vol.25 , pp. 230-236
    • Yilmaz, S.1
  • 57
    • 49549123622 scopus 로고    scopus 로고
    • Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining
    • Yu, S. et al. (2008) Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. Bioinformatics, 24, i119-i125.
    • (2008) Bioinformatics , vol.24 , pp. i119-i125
    • Yu, S.1


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