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Volumn 7, Issue 3, 2015, Pages 214-230

Walking on multiple disease-gene networks to prioritize candidate genes

Author keywords

data fusion; disease gene network; gene prioritization; random walk

Indexed keywords

ARTICLE; DISEASES; EXOME; GENE IDENTIFICATION; GENETICS; GENOMICS; GENOTYPE; PGWALK; PHENOTYPE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL PARAMETERS; AUTISM; CLUSTER ANALYSIS; DNA MUTATIONAL ANALYSIS; EPILEPSY; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC ASSOCIATION STUDY; GENETIC PREDISPOSITION; HUMAN; RECEIVER OPERATING CHARACTERISTIC;

EID: 84938852790     PISSN: 16742788     EISSN: 17594685     Source Type: Journal    
DOI: 10.1093/jmcb/mjv008     Document Type: Article
Times cited : (62)

References (49)
  • 1
    • 25444482801 scopus 로고    scopus 로고
    • Speeding disease gene discovery by sequence based candidate prioritization
    • Adie, E.A., Adams, R.R., Evans, K.L., 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    Adams, R.R.2    Evans, K.L.3
  • 2
    • 33646568805 scopus 로고    scopus 로고
    • Gene prioritization through genomic data fusion
    • Aerts, S., Lambrechts, D., Maity, 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    Lambrechts, D.2    Maity, S.3
  • 4
    • 9144232912 scopus 로고    scopus 로고
    • UniProt: The Universal Protein knowledgebase
    • Apweiler, R., Bairoch, A., Wu, C.H., et al. (2004). UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32, D115-D119.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D115-D119
    • Apweiler, R.1    Bairoch, A.2    Wu, C.H.3
  • 5
    • 0035752429 scopus 로고    scopus 로고
    • Effective mapping of biomedical text to the UMLS Metathesaurus: The MetaMap program
    • Aronson, A.R. (2001). Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc. AMIA Symp. 17-21.
    • (2001) Proc. AMIA Symp. , pp. 17-21
    • Aronson, A.R.1
  • 6
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • The Gene Ontology Consortium
    • Ashburner, M., Ball, C.A., Blake, J.A., 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    Ball, C.A.2    Blake, J.A.3
  • 7
    • 80054746492 scopus 로고    scopus 로고
    • Exome sequencing as a tool for Mendelian disease gene discovery
    • Bamshad, M.J., Ng, S.B., Bigham, A.W., et al. (2011). Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745-755.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 745-755
    • Bamshad, M.J.1    Ng, S.B.2    Bigham, A.W.3
  • 8
    • 9144257886 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Bateman, A., Coin, L., Durbin, R., et al. (2004). The Pfam protein families database. Nucleic Acids Res. 32, D138-D141.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D138-D141
    • Bateman, A.1    Coin, L.2    Durbin, R.3
  • 9
    • 2442604715 scopus 로고    scopus 로고
    • The genetic association database
    • Becker, K.G., Barnes, K.C., Bright, T.J., et al. (2004). The genetic association database. Nat. Genet. 36, 431-432.
    • (2004) Nat. Genet. , vol.36 , pp. 431-432
    • Becker, K.G.1    Barnes, K.C.2    Bright, T.J.3
  • 10
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 11
    • 38549124383 scopus 로고    scopus 로고
    • The microRNA.org resource: Targets and expression
    • Betel, D., Wilson, M., Gabow, A., et al. (2008). The microRNA.org resource: targets and expression. Nucleic Acids Res. 36, D149-D153.
    • (2008) Nucleic Acids Res. , vol.36 , pp. D149-D153
    • Betel, D.1    Wilson, M.2    Gabow, A.3
  • 12
    • 79959486836 scopus 로고    scopus 로고
    • Uncover disease genes by maximizing information flow in the phenome-interactome network
    • Chen, Y., Jiang, T., and Jiang, R. (2011). Uncover disease genes by maximizing information flow in the phenome-interactome network. Bioinformatics 27, i167-i176.
    • (2011) Bioinformatics , vol.27 , pp. i167-i176
    • Chen, Y.1    Jiang, T.2    Jiang, R.3
  • 13
    • 37349068664 scopus 로고    scopus 로고
    • A map of human cancer signaling
    • Cui, Q., Ma, Y., Jaramillo, M., et al. (2007). A map of human cancer signaling. Mol. Syst. Biol. 3, 152.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 152
    • Cui, Q.1    Ma, Y.2    Jaramillo, M.3
  • 14
    • 41349095280 scopus 로고    scopus 로고
    • Genetics of gene expression and its effect on disease
    • Emilsson, V., Thorleifsson, G., Zhang, B., et al. (2008). Genetics of gene expression and its effect on disease. Nature 452, 423-428.
    • (2008) Nature , vol.452 , pp. 423-428
    • Emilsson, V.1    Thorleifsson, G.2    Zhang, B.3
  • 15
    • 84884130368 scopus 로고    scopus 로고
    • De novo mutations in epileptic encephalopathies
    • Epi4K Consortium & Epilepsy Phenome/Genome Project. (2013). De novo mutations in epileptic encephalopathies. Nature 501, 217-221.
    • (2013) Nature , vol.501 , pp. 217-221
    • Epilepsy Phenome/Genome Project1
  • 16
    • 0037580196 scopus 로고    scopus 로고
    • A similarity-based method for genome-wide prediction of disease-relevant human genes
    • Freudenberg, J., and Propping, P. (2002). A similarity-based method for genome-wide 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
    • 84902135948 scopus 로고    scopus 로고
    • Correlating information contents of gene ontology terms to infer semantic similarity of gene products
    • Gan, M. (2014). Correlating information contents of gene ontology terms to infer semantic similarity of gene products. Comput. Math. Methods Med. 2014, 891842.
    • (2014) Comput. Math. Methods Med. , vol.2014
    • Gan, M.1
  • 18
    • 67849095416 scopus 로고    scopus 로고
    • BioMart Central Portal - Unified access to biological data
    • Haider, S., Ballester, B., Smedley, D., et al. (2009). BioMart Central Portal - unified access to biological data. Nucleic Acids Res. 37, W23-W27.
    • (2009) Nucleic Acids Res. , vol.37 , pp. W23-W27
    • Haider, S.1    Ballester, B.2    Smedley, D.3
  • 19
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh, A., Scott, A.F., Amberger, J.S., et al. (2005). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33, D514-D517.
    • (2005) Nucleic Acids Res. , vol.33 , pp. D514-D517
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3
  • 20
    • 77952888699 scopus 로고    scopus 로고
    • De novo mutations of SETBP1 cause Schinzel-Giedion syndrome
    • Hoischen, A., van Bon, B.W., Gilissen, C., et al. (2010). De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat. Genet. 42, 483-485.
    • (2010) Nat. Genet. , vol.42 , pp. 483-485
    • Hoischen, A.1    Van Bon, B.W.2    Gilissen, C.3
  • 21
    • 79960909421 scopus 로고    scopus 로고
    • De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome
    • Hoischen, A., van Bon, B.W., Rodriguez-Santiago, B., et al. (2011). De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome. Nat. Genet. 43, 729-731.
    • (2011) Nat. Genet. , vol.43 , pp. 729-731
    • Hoischen, A.1    Van Bon, B.W.2    Rodriguez-Santiago, B.3
  • 22
    • 84870383937 scopus 로고    scopus 로고
    • Constructing a gene semantic similarity network for the inference of disease genes
    • Jiang, R., Gan, M., and He, P. (2011). Constructing a gene semantic similarity network for the inference of disease genes. BMC Syst. Biol. 5(Suppl 2),S2.
    • (2011) BMC Syst. Biol. , vol.5 , pp. S2
    • Jiang, R.1    Gan, M.2    He, P.3
  • 23
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 24
  • 25
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Köhler, S., Bauer, S., Horn, D., et al. (2008). Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet. 82, 949-958.
    • (2008) Am. J. Hum. Genet. , vol.82 , pp. 949-958
    • Köhler, S.1    Bauer, S.2    Horn, D.3
  • 26
    • 33947095027 scopus 로고    scopus 로고
    • A human phenome-interactome network of protein complexes implicated in genetic disorders
    • Lage, K., Karlberg, E.O., Storling, Z.M., 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    Karlberg, E.O.2    Storling, Z.M.3
  • 27
    • 77952808324 scopus 로고    scopus 로고
    • Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network
    • Li, Y., and Patra, J.C. (2010). Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network. Bioinformatics 26, 1219-1224.
    • (2010) Bioinformatics , vol.26 , pp. 1219-1224
    • Li, Y.1    Patra, J.C.2
  • 28
    • 82555194140 scopus 로고    scopus 로고
    • A mutation screen in patients with Kabuki syndrome
    • Li, Y., Bogershausen, N., Alanay, Y., et al. (2011). A mutation screen in patients with Kabuki syndrome. Hum. Genet. 130, 715-724.
    • (2011) Hum. Genet. , vol.130 , pp. 715-724
    • Li, Y.1    Bogershausen, N.2    Alanay, Y.3
  • 29
    • 84863531160 scopus 로고    scopus 로고
    • PSI-Search: Iterative HOE-reduced profile SSEARCH searching
    • Li, W., McWilliam, H., Goujon, M., et al. (2012). PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics 28, 1650-1651.
    • (2012) Bioinformatics , vol.28 , pp. 1650-1651
    • Li, W.1    McWilliam, H.2    Goujon, M.3
  • 31
    • 0033927616 scopus 로고    scopus 로고
    • Medical Subject Headings (MeSH)
    • Lipscomb, C.E. (2000). Medical Subject Headings (MeSH). Bull. Med. Libr. Assoc. 88, 265-266.
    • (2000) Bull. Med. Libr. Assoc. , vol.88 , pp. 265-266
    • Lipscomb, C.E.1
  • 32
    • 3543106033 scopus 로고    scopus 로고
    • Genome-wide identification of genes likely to be involved in human genetic disease
    • Lopez-Bigas, N., and Ouzounis, C.A. (2004). Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res. 32, 3108-3114.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3108-3114
    • Lopez-Bigas, N.1    Ouzounis, C.A.2
  • 33
    • 0037208166 scopus 로고    scopus 로고
    • TRANSFAC: Transcriptional regulation, from patterns to profiles
    • Matys, V., Fricke, E., Geffers, R., et al. (2003). TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 374-378
    • Matys, V.1    Fricke, E.2    Geffers, R.3
  • 34
    • 42349112088 scopus 로고    scopus 로고
    • Genome-wide association studies for complex traits: Consensus, uncertainty and challenges
    • McCarthy, M.I., Abecasis, G.R., Cardon, L.R., et al. (2008). Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 9, 356-369.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 356-369
    • McCarthy, M.I.1    Abecasis, G.R.2    Cardon, L.R.3
  • 35
    • 84863987708 scopus 로고    scopus 로고
    • Computational tools for prioritizing candidate genes: Boosting disease gene discovery
    • Moreau, Y., and Tranchevent, L.C. (2012). Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat. Rev. Genet. 13, 523-536.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 523-536
    • Moreau, Y.1    Tranchevent, L.C.2
  • 36
    • 84860741138 scopus 로고    scopus 로고
    • Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
    • O'Roak, B.J., Vives, L., Girirajan, S., et al. (2012). Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246-250.
    • (2012) Nature , vol.485 , pp. 246-250
    • O'Roak, B.J.1    Vives, L.2    Girirajan, S.3
  • 37
    • 79959378465 scopus 로고    scopus 로고
    • Family-based designs for genome-wide association studies
    • Ott, J., Kamatani, Y., and Lathrop, M. (2011). Family-based designs for genome-wide association studies. Nat. Rev. Genet. 12, 465-474.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 465-474
    • Ott, J.1    Kamatani, Y.2    Lathrop, M.3
  • 38
    • 84954358609 scopus 로고    scopus 로고
    • The Human Phenotype Ontology: A tool for annotating and analyzing human hereditary disease
    • Robinson, P.N., Kohler, S., Bauer, S., 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    Kohler, S.2    Bauer, S.3
  • 39
    • 0034666108 scopus 로고    scopus 로고
    • STRING: A web-serverto retrieve and display the repeatedly occurring neighbourhood of a gene
    • Snel, B., Lehmann, G., Bork, P., et al. (2000). STRING: a web-serverto retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 28, 3442-3444.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 3442-3444
    • Snel, B.1    Lehmann, G.2    Bork, P.3
  • 40
    • 0345822598 scopus 로고    scopus 로고
    • The positive false discovery rate: A Bayesian interpretation and the q-value
    • Storey, J.D. (2003). The positive false discovery rate: a Bayesian interpretation and the q-value. Ann. Stat. 31, 2013-2035.
    • (2003) Ann. Stat. , vol.31 , pp. 2013-2035
    • Storey, J.D.1
  • 41
    • 11144358198 scopus 로고    scopus 로고
    • A gene atlas of the mouse and human protein-encoding transcriptomes
    • Su, A.I., Wiltshire, T., Batalov, S., et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA 101, 6062-6067.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6062-6067
    • Su, A.I.1    Wiltshire, T.2    Batalov, S.3
  • 42
    • 15044341082 scopus 로고    scopus 로고
    • Integration of text- and datamining using ontologies successfully selects disease gene candidates
    • Tiffin, N., Kelso, J.F., Powell, A.R., et al. (2005). Integration of text- and datamining 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    Kelso, J.F.2    Powell, A.R.3
  • 43
    • 1542787787 scopus 로고    scopus 로고
    • POCUS: Mining genomic sequence annotation to predict disease genes
    • Turner, F.S., Clutterbuck, D.R., and Semple, C.A. (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    Clutterbuck, D.R.2    Semple, C.A.3
  • 45
    • 76749134818 scopus 로고    scopus 로고
    • Associating genes and protein complexes with disease via network propagation
    • Vanunu, O., Magger, O., Ruppin, E., et al.(2010). Associating genes and protein complexes with disease via network propagation. PLoS Comput. Biol. 6, e1000641.
    • (2010) PLoS Comput. Biol. , vol.6
    • Vanunu, O.1    Magger, O.2    Ruppin, E.3
  • 46
    • 43249114206 scopus 로고    scopus 로고
    • Network-based global inference of human disease genes
    • Wu, X., Jiang, R., Zhang, M.Q., 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    Jiang, R.2    Zhang, M.Q.3
  • 47
    • 58049220319 scopus 로고    scopus 로고
    • Align human interactome with phenome to identify causative genes and networks underlying disease families
    • Wu, X., Liu, Q., and Jiang, R. (2009). Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinformatics 25, 98-104.
    • (2009) Bioinformatics , vol.25 , pp. 98-104
    • Wu, X.1    Liu, Q.2    Jiang, R.3
  • 48
    • 84897463218 scopus 로고    scopus 로고
    • Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies
    • Wu, J., Li, Y., and Jiang, R. (2014). Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies. PLoS Genet. 10, e1004237.
    • (2014) PLoS Genet. , vol.10
    • Wu, J.1    Li, Y.2    Jiang, R.3
  • 49
    • 77649105221 scopus 로고    scopus 로고
    • Distribution of Fisher's combination statistic when the tests are dependent
    • Yang, J.J. (2010). Distribution of Fisher's combination statistic when the tests are dependent. J. Stat. Comput. Simul. 80, 1-12.
    • (2010) J. Stat. Comput. Simul. , vol.80 , pp. 1-12
    • Yang, J.J.1


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