Prioritizing disease candidate genes by a gene interconnectedness-based approach

10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet)

Volumn 12, Issue SUPPL. 3, 2011, Pages

  Hsu, Chia Lang ^a   Huang, Yen Hua ^a   Hsu, Chien Ting ^a   Yang, Ueng Cheng ^a  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; CANDIDATE GENES; DISEASE GENES; EXPERIMENTAL APPROACHES; LINKAGE ANALYSIS; NETWORK DATA; NETWORK-BASED; NETWORK-BASED TOOLS; PARAMETER-FREE METHODS; PROTEIN-PROTEIN INTERACTION NETWORKS; TEST SCENARIO; USER-FRIENDLY METHODS;

BIOINFORMATICS; PROTEINS; WEBSITES;

GENES;

ALGORITHM; ARTICLE; DISEASES; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC LINKAGE; GENETICS; HUMAN; HUMAN GENOME; METHODOLOGY;

ALGORITHMS; DATABASES, GENETIC; DISEASE; GENETIC ASSOCIATION STUDIES; GENETIC LINKAGE; GENOME, HUMAN; HUMANS;

EID: 84862249788     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1186/1471-2164-12-S3-S25     Document Type: Conference Paper

References (53)

1. Kuhlenbaumer G, Hullmann J, Appenzeller S: Novel genomic techniques open new avenues in the analysis of monogenic disorders. Hum Mutat 2011, 32(2):144-151.
2. Tang WC, Yap MK, Yip SP: A review of current approaches to identifying human genes involved in myopia. Clin Exp Optom 2008, 91(1):4-22.
3. Botstein D, Risch N: Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 2003, 33(Suppl):228-237.
4. Glazier AM, Nadeau JH, Aitman TJ: Finding genes that underlie complex traits. Science 2002, 298(5602):2345-2349.
5. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN: Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 2008, 9(5):356-369.
6. Oti M, Brunner HG: The modular nature of genetic diseases. Clin Genet 2007, 71(1):1-11.
7. Zhu M, Zhao S: Candidate gene identification approach: progress and challenges. Int J Biol Sci 2007, 3(7):420-427.
8. Kann MG: Advances in translational bioinformatics: computational approaches for the hunting of disease genes. Brief Bioinform 2010, 11(1):96-110.
9. Tranchevent LC, Capdevila FB, Nitsch D, De Moor B, De Causmaecker P, Moreau Y: A guide to web tools to prioritize candidate genes. Brief Bioinform 2011, 12(1):22-32.
10. Ideker T, Sharan R: Protein networks in disease. Genome Res 2008, 18(4):644-652.
11. Chen JY, Shen C, Sivachenko AY: Mining Alzheimer disease relevant proteins from integrated protein interactome data. Pac Symp Biocomput 2006, 367-378.
12. Oti M, Snel B, Huynen MA, Brunner HG: Predicting disease genes using protein-protein interactions. J Med Genet 2006, 43(8):691-698.
13. Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A: Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc Natl Acad Sci U S A 2004, 101(42):15148-15153.
14. Franke L, van Bakel H, Fokkens L, de Jong ED, Egmont-Petersen M, Wijmenga C: Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet 2006, 78(6):1011-1025.
15. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, et al: A human phenomeinteractome network of protein complexes implicated in genetic disorders. Nat Biotechnol 2007, 25(3):309-316.
16. Wu X, Jiang R, Zhang MQ, Li S: Network-based global inference of human disease genes. Mol Syst Biol 2008, 4:189.
17. Kohler S, Bauer S, Horn D, Robinson PN: Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 2008, 82(4):949-958.
18. Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R: Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol 2010, 6(1):e1000641.
19. Chen J, Aronow BJ, Jegga AG: Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 2009, 10:73.
20. Chen X, Yan GY, Liao XP: A novel candidate disease genes prioritization method based on module partition and rank fusion. OMICS 2010, 14(4):337-356.
21. Sun PG, Gao L, Han S: Prediction of human disease-related gene clusters by clustering analysis. Int J Biol Sci 2011, 7(1):61-73.
22. Lin J, Gan CM, Zhang X, Jones S, Sjoblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, et al: A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res 2007, 17(9):1304-1318.
23. Carlson MR, Zhang B, Fang Z, Mischel PS, Horvath S, Nelson SF: Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics 2006, 7:40.
24. Oldham MC, Horvath S, Geschwind DH: Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A 2006, 103(47):17973-17978.
25. Navlakha S, Kingsford C: The power of protein interaction networks for associating genes with diseases. Bioinformatics 2010, 26(8):1057-1063.
26. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The database of interacting proteins: 2004 update. Nucleic Acids Res 2004, 32(Database issue):D449-D451.
27. Alfarano C, Andrade CE, 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 2005, 33(Database issue):D418-D424.
28. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, et al: The IntAct molecular interaction database in 2010. Nucleic Acids Res 2010, 38(Database issue):D525-531.
29. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, et al: The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21(6):832-834.
30. Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G: MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2010, 38(Database issue):D532-539.
31. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al: Human Protein Reference Database-2009 update. Nucleic Acids Res 2009, 37(Database issue):D767-D772.
32. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, 34(Database issue):D535-539.
33. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, et al: Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009, 37(Database issue):D619-622.
34. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C: Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 2011, 39(Database issue):D685-690.
35. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, et al: STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009, 37(Database issue):D412-416.
36. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B: STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31(1):258-261.
37. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33(Database issue): D514-D517.
38. Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-113.
39. Chung MY, Lu YC, Cheng NC, Soong BW: A novel autosomal dominant spinocerebellar ataxia (SCA22) linked to chromosome 1p21-q23. Brain 2003, 126(Pt 6):1293-1299.
40. Duenas AM, Goold R, Giunti P: Molecular pathogenesis of spinocerebellar ataxias. Brain 2006, 129(Pt 6):1357-1370.
41. Matilla-Duenas A, Sanchez I, Corral-Juan M, Davalos A, Alvarez R, Latorre P: Cellular and molecular pathways triggering neurodegeneration in the spinocerebellar ataxias. Cerebellum 2010, 9(2):148-166.
42. Schols L, Bauer P, Schmidt T, Schulte T, Riess O: Autosomal dominant cerebellar ataxias: clinical features, genetics, and pathogenesis. Lancet Neurol 2004, 3(5):291-304.
43. Lim J, Hao T, Shaw C, Patel AJ, Szabo G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, et al: A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 2006, 125(4):801-814.
44. Ikeda Y, Dick KA, Weatherspoon MR, Gincel D, Armbrust KR, Dalton JC, Stevanin G, Durr A, Zuhlke C, Burk K, et al: Spectrin mutations cause spinocerebellar ataxia type 5. Nat Genet 2006, 38(2):184-190.
45. Lorenzo DN, Li MG, Mische SE, Armbrust KR, Ranum LP, Hays TS: Spectrin mutations that cause spinocerebellar ataxia type 5 impair axonal transport and induce neurodegeneration in Drosophila. J Cell Biol 2010, 189(1):143-158.
46. Stankewich MC, Gwynn B, Ardito T, Ji L, Kim J, Robledo RF, Lux SE, Peters LL, Morrow JS: Targeted deletion of betaIII spectrin impairs synaptogenesis and generates ataxic and seizure phenotypes. Proc Natl Acad Sci U S A 2010, 107(13):6022-6027.
47. Clarkson YL, Gillespie T, Perkins EM, Lyndon AR, Jackson M: Beta-III spectrin mutation L253P associated with spinocerebellar ataxia type 5 interferes with binding to Arp1 and protein trafficking from the Golgi. Hum Mol Genet 2010, 19(18):3634-3641.
48. Sun G, Tomita H, Shakkottai VG, Gargus JJ: Genomic organization and promoter analysis of human KCNN3 gene. J Hum Genet 2001, 46(8):463-470.
49. Grube S, Gerchen MF, Adamcio B, Pardo LA, Martin S, Malzahn D, Papiol S, Begemann M, Ribbe K, Friedrichs H, et al: A CAG repeat polymorphism of KCNN3 predicts SK3 channel function and cognitive performance in schizophrenia. EMBO Mol Med 2011, 3(6):309-319.
50. Jin DK, Hwang HZ, Oh MR, Kim JS, Lee M, Kim S, Lim SW, Seo MY, Kim JH, Kim DK: CAG repeats of CTG18.1 and KCNN3 in Korean patients with bipolar affective disorder. J Affect Disord 2001, 66(1):19-24.
51. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, et al: Gene prioritization through genomic data fusion. Nat Biotechnol 2006, 24(5):537-544.
52. Li Y, Patra JC: Integration of multiple data sources to prioritize candidate genes using discounted rating system. BMC Bioinformatics 2010, 11(Suppl 1):S20.
53. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL: The human disease network. Proc Natl Acad Sci U S A 2007, 104(21):8685-8690.