The orphan disease networks

American Journal of Human Genetics

Volumn 88, Issue 6, 2011, Pages 755-766

  Zhang, Minlu ^a,c   Zhu, Cheng ^a   Jacomy, Alexis ^d   Lu, Long J ^a,b,c   Jegga, Anil G ^a,b,c  

^a University of Cincinnati   (United States)

^b UNIVERSITY OF CINCINNATI   (United States)

^c CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^d WebAtlas   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; DIAGNOSTIC APPROACH ROUTE; GENE CONSTRUCT; GENE EXPRESSION; GENE FUNCTION; GENE INACTIVATION; GENE MUTATION; GENETIC ANALYSIS; GENETIC DISORDER; HUMAN; ORPHAN DISEASE; PHENOTYPE; PRIORITY JOURNAL; PROTEIN INTERACTION; RARE DISEASE;

ANIMALS; GENE REGULATORY NETWORKS; HUMANS; MICE; MICE, KNOCKOUT; MUTATION; RARE DISEASES;

EID: 79958811512     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2011.05.006     Document Type: Article

References (41)

1. J.W. Dear, P. Lilitkarntakul, and D.J. Webb Are rare diseases still orphans or happily adopted? The challenges of developing and using orphan medicinal products Br. J. Clin. Pharmacol. 62 2006 264 271 (Pubitemid 44215525)
2. P. Stolk, M.J. Willemen, and H.G. Leufkens Rare essentials: Drugs for rare diseases as essential medicines Bull. World Health Organ. 84 2006 745 751 (Pubitemid 44482401)
3. A. Schieppati, J.I. Henter, E. Daina, and A. Aperia Why rare diseases are an important medical and social issue Lancet 371 2008 2039 2041 (Pubitemid 351799861)
4. S. Aymé, and J. Schmidtke Networking for rare diseases: A necessity for Europe Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 50 2007 1477 1483
5. M.E. Haffner Adopting orphan drugs - two dozen years of treating rare diseases N. Engl. J. Med. 354 2006 445 447 (Pubitemid 43200295)
6. G. Remuzzi, and S. Garattini Rare diseases: What's next? Lancet 371 2008 1978 1979 (Pubitemid 351799846)
7. H.E. Heemstra, S. van Weely, H.A. Büller, H.G. Leufkens, and R.L. de Vrueh Translation of rare disease research into orphan drug development: Disease matters Drug Discov. Today 14 2009 1166 1173
8. I. Feldman, A. Rzhetsky, and D. Vitkup Network properties of genes harboring inherited disease mutations Proc. Natl. Acad. Sci. USA 105 2008 4323 4328 (Pubitemid 351754379)
9. K.I. Goh, M.E. Cusick, D. Valle, B. Childs, M. Vidal, and A.L. Barabási The human disease network Proc. Natl. Acad. Sci. USA 104 2007 8685 8690 (Pubitemid 47175372)
10. M.A. Yildirim, K.I. Goh, M.E. Cusick, A.L. Barabási, and M. Vidal Drug-target network Nat. Biotechnol. 25 2007 1119 1126 (Pubitemid 47538114)
11. M. Oti, M.A. Huynen, and H.G. Brunner The biological coherence of human phenome databases Am. J. Hum. Genet. 85 2009 801 808
12. B. Linghu, E.S. Snitkin, Z. Hu, Y. Xia, and C. Delisi Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network Genome Biol. 10 2009 R91
13. S. Aymé Orphanet, an information site on rare diseases Soins 672 2003 46 47
14. A. Hamosh, A.F. Scott, J. Amberger, D. Valle, and V.A. McKusick Online Mendelian Inheritance in Man (OMIM) Hum. Mutat. 15 2000 57 61 (Pubitemid 30036170)
15. R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, and M. Magrane UniProt: The Universal Protein knowledgebase Nucleic Acids Res. 32 Database issue 2004 D115 D119
16. U. Stelzl, U. Worm, M. Lalowski, C. Haenig, F.H. Brembeck, H. Goehler, M. Stroedicke, M. Zenkner, A. Schoenherr, and S. Koeppen A human protein-protein interaction network: A resource for annotating the proteome Cell 122 2005 957 968 (Pubitemid 41345212)
17. J.F. Rual, K. Venkatesan, T. Hao, T. Hirozane-Kishikawa, A. Dricot, N. Li, G.F. Berriz, F.D. Gibbons, M. Dreze, and N. Ayivi-Guedehoussou Towards a proteome-scale map of the human protein-protein interaction network Nature 437 2005 1173 1178 (Pubitemid 41509356)
18. A.K. Ramani, R.C. Bunescu, R.J. Mooney, and E.M. Marcotte Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome Genome Biol. 6 2005 R40
19. T.S. Prasad, K. Kandasamy, and A. Pandey Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology Methods Mol. Biol. 577 2009 67 79
20. G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, B. Jassal, G.R. Gopinath, G.R. Wu, and L. Matthews Reactome: A knowledgebase of biological pathways Nucleic Acids Res. 33 Database issue 2005 D428 D432
21. C. Alfarano, C.E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, D. Betel, B. Bobechko, K. Boutilier, and E. Burgess The Biomolecular Interaction Network Database and related tools 2005 update Nucleic Acids Res. 33 Database issue 2005 D418 D424
22. J.A. Blake, J.E. Richardson, C.J. Bult, J.A. Kadin, J.T. Eppig Mouse Genome Database Group MGD: The Mouse Genome Database Nucleic Acids Res. 31 2003 193 195 (Pubitemid 36150363)
23. D. Ramsköld, E.T. Wang, C.B. Burge, and R. Sandberg An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data PLoS Comput. Biol. 5 2009 e1000598
24. Z. Tu, L. Wang, M. Xu, X. Zhou, T. Chen, and F. Sun Further understanding human disease genes by comparing with housekeeping genes and other genes BMC Genomics 7 2006 31
25. D.J. Pagliarini, S.E. Calvo, B. Chang, S.A. Sheth, S.B. Vafai, S.E. Ong, G.A. Walford, C. Sugiana, A. Boneh, and W.K. Chen A mitochondrial protein compendium elucidates complex I disease biology Cell 134 2008 112 123 (Pubitemid 351916708)
26. J. Chen, E.E. Bardes, B.J. Aronow, and A.G. Jegga ToppGene Suite for gene list enrichment analysis and candidate gene prioritization Nucleic Acids Res. 37 Web Server issue 2009 W305 W311
27. H. Yu, P.M. Kim, E. Sprecher, V. Trifonov, and M. Gerstein The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics PLoS Comput. Biol. 3 2007 e59
28. M. Girvan, and M.E. Newman Community structure in social and biological networks Proc. Natl. Acad. Sci. USA 99 2002 7821 7826 (Pubitemid 34650963)
29. K.Y. Yip, H. Yu, P.M. Kim, M. Schultz, and M. Gerstein The tYNA platform for comparative interactomics: A web tool for managing, comparing and mining multiple networks Bioinformatics 22 2006 2968 2970 (Pubitemid 44811577)
30. Bastian, M., Heymann, S., Jacomy, M. (2009). Gephi: An open source software for exploring and manipulating networks. In International AAAI Conference on Weblogs and Social Media. (San Jose, CA: AAAI Publications) (http://gephi.org/publications/gephi-bastian-feb09.pdf ).
31. V.D. Blondel, J. Guillaume, R. Lambiotte, and E. Lefebvre Fast unfolding of communities in large networks J. Stat. Mech. 2008 2008 P10008
32. M. Oti, B. Snel, M.A. Huynen, and H.G. Brunner Predicting disease genes using protein-protein interactions J. Med. Genet. 43 2006 691 698 (Pubitemid 44214908)
33. L. Hakes, J.W. Pinney, D.L. Robertson, and S.C. Lovell Protein-protein interaction networks and biology - what's the connection? Nat. Biotechnol. 26 2008 69 72
34. Field, M.J., and Boat, T.F. (2010). Rare diseases and orphan products: Accelerating research and development. In Rare Diseases and Orphan Products: Accelerating Research and Development, M.J. Field and T.F. Boat, eds. Committee on Accelerating Rare Diseases Research and Orphan Product Development, Institute of Medicine (Washington DC: The National Academies Press).
35. S.J. Bowne, Q. Liu, L.S. Sullivan, J. Zhu, C.J. Spellicy, C.B. Rickman, E.A. Pierce, and S.P. Daiger Why do mutations in the ubiquitously expressed housekeeping gene IMPDH1 cause retina-specific photoreceptor degeneration? Invest. Ophthalmol. Vis. Sci. 47 2006 3754 3765 (Pubitemid 46044287)
36. A.L. Barabási, and Z.N. Oltvai Network biology: Understanding the cell's functional organization Nat. Rev. Genet. 5 2004 101 113 (Pubitemid 38160277)
37. S. Suthram, J.T. Dudley, A.P. Chiang, R. Chen, T.J. Hastie, and A.J. Butte Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets PLoS Comput. Biol. 6 2010 e1000662
38. Y. Li, and P. Agarwal A pathway-based view of human diseases and disease relationships PLoS ONE 4 2009 e4346
39. D. Hristovski, B. Peterlin, J.A. Mitchell, and S.M. Humphrey Using literature-based discovery to identify disease candidate genes Int. J. Med. Inform. 74 2005 289 298 (Pubitemid 40208459)
40. I. Lee, B. Lehner, T. Vavouri, J. Shin, A.G. Fraser, and E.M. Marcotte Predicting genetic modifier loci using functional gene networks Genome Res. 20 2010 1143 1153
41. M.A. Pujana, J.D. Han, L.M. Starita, K.N. Stevens, M. Tewari, J.S. Ahn, G. Rennert, V. Moreno, T. Kirchhoff, and B. Gold Network modeling links breast cancer susceptibility and centrosome dysfunction Nat. Genet. 39 2007 1338 1349 (Pubitemid 350035000)