A human phenome-interactome network of protein complexes implicated in genetic disorders
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Brunner, H.G. & van Driel, M.A. From syndrome families to functional genomics. Nat. Rev. Genet. 5, 545–551 (2004).
Adie, E.A., Adams, R.R., Evans, K.L., Porteous, D.J. & Pickard, B.S. Speeding disease gene discovery by sequence-based candidate prioritization. BMC Bioinformatics 6, 55 (2005).
Franke, L. et al. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78, 1011–1025 (2006).
Franke, L. et al. TEAM: a tool for the integration of expression, and linkage and association maps. Eur. J. Hum. Genet. 12, 633–638 (2004).
Turner, F.S., Clutterbuck, D.R. & Semple, C.A. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol. 4, R75 (2003).
Perez-Iratxeta, C., Bork, P. & Andrade, M.A. Association of genes to genetically inherited diseases using data mining. Nat. Genet. 31, 316–319 (2002).
Perez-Iratxeta, C., Wjst, M., Bork, P. & Andrade, M.A. G2D: a tool for mining genes associated with disease. BMC Genet. 6, 45 (2005).
Masseroli, M., Galati, O. & Pinciroli, F. GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res. 33, W717–W723 (2005).
van Driel, M.A., Cuelenaere, K., Kemmeren, P.P., Leunissen, J.A. & Brunner, H.G. A new web-based data mining tool for the identification of candidate genes for human genetic disorders. Eur. J. Hum. Genet. 11, 57–63 (2003).
van Driel, M.A. et al. GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. Nucleic Acids Res. 33, W758–761 (2005).
Hristovski, D., Peterlin, B., Mitchell, J.A. & Humphrey, S.M. Using literature-based discovery to identify disease candidate genes. Int. J. Med. Inform. 74, 289–298 (2005).
Freudenberg, J. & Propping, P. A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics 18 Suppl 2, S110–S115 (2002).
Barabasi, A.L. & Oltvai, Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101–113 (2004).
van Driel, M.A., Bruggeman, J., Vriend, G., Brunner, H.G. & Leunissen, J.A. A text-mining analysis of the human phenome. Eur. J. Hum. Genet. 14, 535–542 (2006).
Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736 (2003).
Walhout, A.J. et al. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12, 1952–1958 (2002).
Boulton, S.J. et al. Combined functional genomic maps of the C. elegans DNA damage response. Science 295, 127–131 (2002).
Gandhi, T.K. et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet. 38, 285–293 (2006).
Lim, J. et al. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125, 801–814 (2006).
Oti, M., Snel, B., Huynen, M.A. & Brunner, H.G. Predicting disease genes using protein-protein interactions. J. Med. Genet. (2006).
Aerts, S. et al. Gene prioritization through genomic data fusion. Nat. Biotechnol. 24, 537–544 (2006).
von Mering, C. et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399–403 (2002).
Rual, J.F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178 (2005).
Stelzl, U. et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968 (2005).
Korbel, J.O. et al. Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol. 3, e134 (2005).
Schijvenaars, B.J. et al. Thesaurus-based disambiguation of gene symbols. BMC Bioinformatics 6, 149 (2005).
Butte, A.J. & Kohane, I.S. Creation and implications of a phenome-genome network. Nat. Biotechnol. 24, 55–62 (2006).
Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A. & McKusick, V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33 (Database Issue), D514–D517 (2005).
Aronson, A.R. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc. AMIA Symp. 17–21 (2001).
Bodenreider, O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32, D267–D270 (2004).
Gerard Salton, M.J.M. Introduction to Modern Information Retrieval (Neal-Schuman Publishers, New York, 1983).
Divita, G., Tse, T. & Roth, L. Failure analysis of MetaMap Transfer (MMTx). Medinfo 11, 763–767 (2004).
Gu, S., Kumaramanickavel, G., Srikumari, C.R., Denton, M.J. & Gal, A. Autosomal recessive retinitis pigmentosa locus RP28 maps between D2S1337 and D2S286 on chromosome 2p11–p15 in an Indian family. J. Med. Genet. 36, 705–707 (1999).
Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569–4574 (2001).
Sohocki, M.M. et al. A range of clinical phenotypes associated with mutations in CRX, a photoreceptor transcription-factor gene. Am. J. Hum. Genet. 63, 1307–1315 (1998).
Sekine, M. et al. Localization of a novel susceptibility gene for familial ovarian cancer to chromosome 3p22–p25. Hum. Mol. Genet. 10, 1421–1429 (2001).
Demuth, I. et al. An inducible null mutant murine model of Nijmegen breakage syndrome proves the essential function of NBS1 in chromosomal stability and cell viability. Hum. Mol. Genet. 13, 2385–2397 (2004).
Matsuura, S. et al. Positional cloning of the gene for Nijmegen breakage syndrome. Nat. Genet. 19, 179–181 (1998).
Castilla, L.H. et al. Mutations in the BRCA1 gene in families with early-onset breast and ovarian cancer. Nat. Genet. 8, 387–391 (1994).
Lancaster, J.M. et al. BRCA2 mutations in primary breast and ovarian cancers. Nat. Genet. 13, 238–240 (1996).
Taniguchi, T. et al. Disruption of the Fanconi anemia–BRCA pathway in cisplatin-sensitive ovarian tumors. Nat. Med. 9, 568–574 (2003).
Dechairo, B. et al. Replication and extension studies of inflammatory bowel disease susceptibility regions confirm linkage to chromosome 6p (IBD3). Eur. J. Hum. Genet. 9, 627–633 (2001).
Hampe, J. et al. Linkage of inflammatory bowel disease to human chromosome 6p. Am. J. Hum. Genet. 65, 1647–1655 (1999).
Hosler, B.A. et al. Linkage of familial amyotrophic lateral sclerosis with frontotemporal dementia to chromosome 9q21–q22. J.A.M.A. 284, 1664–1669 (2000).
Koyama, S. et al. Alteration of familial ALS-linked mutant SOD1 solubility with disease progression: its modulation by the proteasome and Hsp70. Biochem. Biophys. Res. Commun. 343, 719–730 (2006).
Polavarapu, N. et al. Investigation into biomedical literature classification using support vector machines. Proc. IEEE Comput. Syst. Bioinform. Conf., 366–374 (8-11 August 2005).
Bader, G.D., Betel, D. & Hogue, C.W. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248–250 (2003).
Hermjakob, H. et al. IntAct: an open source molecular interaction database. Nucleic Acids Res. 32 (Database Issue), D452–D455 (2004).
Kanehisa, M. et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354–D357 (2006).
Joshi-Tope, G. et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33, D428–D432 (2005).
Walhout, A.J. et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287, 116–122 (2000).