Walking the Interactome for Prioritization of Candidate Disease Genes

American Journal of Human Genetics

Volumn 82, Issue 4, 2008, Pages 949-958

  Köhler, Sebastian ^a   Bauer, Sebastian ^a   Horn, Denise ^a   Robinson, Peter N ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; CLONING; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENETIC DISORDER; GENETIC LINKAGE; HUMAN; MULTIGENE FAMILY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIMULATION;

ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENETIC DISEASES, INBORN; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INTERNET; LINKAGE (GENETICS); MICE; PEDIGREE; PROTEIN INTERACTION MAPPING; SOFTWARE;

EID: 41549139527     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2008.02.013     Document Type: Article

References (44)

1. Hamosh A., Scott A.F., Amberger J., Bocchini C., Valle D., and McKusick V.A. Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 30 (2002) 52-55
2. Brunner H.G., and van Driel M.A. From syndrome families to functional genomics. Nat. Rev. Genet. 5 (2004) 545-551
3. Glazier A.M., Nadeau J.H., and Aitman T.J. Finding genes that underlie complex traits. Science 298 (2002) 2345-2349
4. Botstein D., and Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33 Suppl (2003) 228-237
5. Perez-Iratxeta C., Bork P., and Andrade M.A. Association of genes to genetically inherited diseases using data mining. Nat. Genet. 31 (2002) 316-319
6. Freudenberg J., and Propping P. A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics 18 (2002) S110-S115
7. van Driel M.A., Cuelenaere K., Kemmeren P.P., Leunissen J.A., and 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 (2003) 57-63
8. Turner F.S., Clutterbuck D.R., and Semple C.A. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol. 4 (2003) R75
9. Tiffin N., Kelso J.F., Powell A.R., Pan H., Bajic V.B., and Hide W.A. Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res. 33 (2005) 1544-1552
10. Aerts S., Lambrechts D., Maity S., Van Loo P., Coessens B., De Smet F., Tranchevent L.-C., De Moor B., Marynen P., Hassan B., et al. Gene prioritization through genomic data fusion. Nat. Biotechnol. 24 (2006) 537-544
11. Franke L., Bakel H., Fokkens L., de Jong E.D., Egmont-Petersen M., and Wijmenga C. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78 (2006) 1011-1025
12. Adie E.A., Adams R.R., Evans K.L., Porteous D.J., and Pickard B.S. SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics 22 (2006) 773-774
13. Adie E.A., Adams R.R., Evans K.L., Porteous D.J., and Pickard B.S. Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics 6 (2005) 55
14. López-Bigas N., and Ouzounis C.A. Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res. 32 (2004) 3108-3114
15. Stelzl U., and Wanker E.E. The value of high quality protein-protein interaction networks for systems biology. Curr. Opin. Chem. Biol. 10 (2006) 551-558
16. Gandhi T.K.B., Zhong J., Mathivanan S., Karthick L., Chandrika K.N., Mohan S.S., Sharma S., Pinkert S., Nagaraju S., Periaswamy B., et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet. 38 (2006) 285-293
17. Oti M., Snel B., Huynen M., and Brunner H.G. Predicting disease genes using protein-protein interactions. J. Med. Genet. 43 (2006) 691-698
18. George R.A., Liu J.Y., Feng L.L., Bryson-Richardson R.J., Fatkin D., and Wouters M.A. Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Res. 34 (2006) e130
19. Maglott D., Ostell J., Pruitt K.D., and Tatusova T. Entrez gene: gene-centered information at ncbi. Nucleic Acids Res. 35 (2007) D26-D31
20. Peri S., Navarro J.D., Kristiansen T.Z., Amanchy R., Surendranath V., Muthusamy B., Gandhi T.K.B., Chandrika K.N., Deshpande N., Suresh S., et al. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 32 (2004) D497-D501
21. Alfarano C., Andrade C.E., Anthony K., Bahroos N., Bajec M., Bantoft K., Betel D., Bobechko B., Boutilier K., Burgess E., et al. The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res. 33 (2005) D418-D424
22. Stark C., Breitkreutz B.-J., Reguly T., Boucher L., Breitkreutz A., and Tyers M. Biogrid: a general repository for interaction datasets. Nucleic Acids Res. 34 (2006) D535-D539
23. Kerrien S., Alam-Faruque Y., Aranda B., Bancarz I., Bridge A., Derow C., Dimmer E., Feuermann M., Friedrichsen A., Huntley R., et al. IntAct-open source resource for molecular interaction data. Nucleic Acids Res. 35 (2007) D561-D565
24. Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., and Eisenberg D. The database of interacting proteins: 2004 update. Nucleic Acids Res. 32 (2004) D449-D451
25. O'Brien K.P., Remm M., and Sonnhammer E.L.L. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33 (2005) D476-D480
26. von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Krger B., Snel B., and Bork P. STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35 (2007) D358-D362
27. von Mering C., Huynen M., Jaeggi D., Schmidt S., Bork P., and Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31 (2003) 258-261
28. Can, T., Çamoǧlu, O., and Singh, A.K. (2005). Analysis of protein-protein interaction networks using random walks. In BIOKDD '05: Proceedings of the 5th international workshop on Bioinformatics (New York, USA: Association for Computing Machinery). 61-68.
29. Kondor, R.I., and Lafferty, J.D. (2002). Diffusion kernels on graphs and other discrete input spaces. In ICML '02: Proceedings of the Nineteenth International Conference on Machine Learning. (San Francisco, CA, USA: Morgan Kaufmann Publishers Inc.), pp. 315-322.
30. Hart G.T., Ramani A.K., and Marcotte E.M. How complete are current yeast and human protein-interaction networks?. Genome Biol. 7 (2006) 120
31. Pagel P., Mewes H.W., and Frishman D. Conservation of protein-protein interactions - lessons from ascomycota. Trends Genet. 20 (2004) 72-76
32. Mendler M., Eich-Bender S.G., Vaughan L., Winterhalter K.H., and Bruckner P. Cartilage contains mixed fibrils of collagen types ii, ix, and xi. J. Cell Biol. 108 (1989) 191-197
33. Lage K., Karlberg E.O., Størling Z.M., Olason P.I., Pedersen A.G., Rigina O., Hinsby A.M., Tümer Z., Pociot F., Tommerup N., et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat. Biotechnol. 25 (2007) 309-316
34. Lee J.M., and Sonnhammer E.L.L. Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 13 (2003) 875-882
35. Barabási A.-L. Network medicine-from obesity to the "diseasome". N. Engl. J. Med. 357 (2007) 404-407
36. Lim J., Hao T., Shaw C., Patel A.J., Szabó G., Rual J.-F., Fisk C.J., Li N., Smolyar A., Hill D.E., et al. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125 (2006) 801-814
37. Attanasio M., Uhlenhaut N.H., Sousa V.H., O'Toole J.F., Otto E., Anlag K., Klugmann C., Treier A.-C., Helou J., Sayer J.A., et al. Loss of GLIS2 causes nephronophthisis in humans and mice by increased apoptosis and fibrosis. Nat. Genet. 39 (2007) 1018-1024
38. Asimaki A., Syrris P., Wichter T., Matthias P., Saffitz J.E., and McKenna W.J. A novel dominant mutation in plakoglobin causes arrhythmogenic right ventricular cardiomyopathy. Am. J. Hum. Genet. 81 (2007) 964-973
39. Chakarova C.F., Papaioannou M.G., Khanna H., Lopez I., Waseem N., Shah A., Theis T., Friedman J., Maubaret C., Bujakowska K., et al. Mutations in TOPORS cause autosomal dominant retinitis pigmentosa with perivascular retinal pigment epithelium atrophy. Am. J. Hum. Genet. 81 (2007) 1098-1103
40. Coppieters F., Leroy B.P., Beysen D., Hellemans J., Bosscher K.D., Haegeman G., Robberecht K., Wuyts W., Coucke P.J., and Baere E.D. Recurrent mutation in the first zinc finger of the orphan nuclear receptor NR2E3 causes autosomal dominant retinitis pigmentosa. Am. J. Hum. Genet. 81 (2007) 147-157
41. Razzaque M.A., Nishizawa T., Komoike Y., Yagi H., Furutani M., Amo R., Kamisago M., Momma K., Katayama H., Nakagawa M., et al. Germline gain-of-function mutations in RAF1 cause Noonan syndrome. Nat. Genet. 39 (2007) 1013-1017
42. Lehmann K., Seemann P., Silan F., Goecke T.O., Irgang S., Kjaer K.W., Kjaergaard S., Mahoney M.J., Morlot S., Reissner C., et al. A new subtype of brachydactyly type B caused by point mutations in the bone morphogenetic protein antagonist NOGGIN. Am. J. Hum. Genet. 81 (2007) 388-396
43. Delague V., Jacquier A., Hamadouche T., Poitelon Y., Baudot C., Boccaccio I., Chouery E., Chaouch M., Kassouri N., Jabbour R., et al. Mutations in FGD4 encoding the Rho GDP/GTP exchange factor FRABIN cause autosomal recessive Charcot-Marie-Tooth type 4H. Am. J. Hum. Genet. 81 (2007) 1-16
44. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., and Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13 (2003) 2498-2504