Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge

Journal of Biomedical Informatics

Volumn 41, Issue 5, 2008, Pages 717-729

  Gudivada, Ranga Chandra ^a,b   Qu, Xiaoyan A ^a,b   Chen, Jing ^a,b   Jegga, Anil G ^b   Neumann, Eric K ^c   Aronow, Bruce J ^a,b  

^a University of Cincinnati   (United States)

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

^c Clinical Semantics Group   (United States)

Author keywords

Bioinformatics; Data integration; NLP; Ontologies; OWL; RDF; Semantic ranking; Semantic Web; SPARQL

Indexed keywords

ARTIFICIAL INTELLIGENCE; DATA STRUCTURES; FILE ORGANIZATION; FLOW INTERACTIONS; GENE EXPRESSION; HEALTH; INFORMATION MANAGEMENT; INFORMATION THEORY; KNOWLEDGE MANAGEMENT; KNOWLEDGE REPRESENTATION; MODEL STRUCTURES; PLANTS (BOTANY); SEMANTIC WEB; SEMANTICS;

BIOCHEMICAL PROPERTIES; BIOINFORMATICS; CANDIDATE GENES; CAUSAL RELATIONSHIPS; CHRONIC DISEASES; CLINICAL FEATURES; DATA INTEGRATION; DIFFERENTIAL GENE EXPRESSIONS; ENVIRONMENTAL FACTORS; ETIOLOGIC FACTORS; EXPRESSION PATTERNS; GENE IDENTIFICATION; GENOMIC STUDIES; GRAPH NETWORKS; INTEGRATIVE GENOMICS; LARGE KNOWLEDGE BASES; MODEL-DRIVEN; MULTIPLE FACTORS; NETWORK DATA; NLP; ONTOLOGIES; OWL; PRIOR KNOWLEDGE; PRIORITIZATION; QUANTITATIVE TRAIT LOCI; RDF; SEMANTIC RANKING; SEMANTIC RELATIONSHIPS; SPARQL; WEB METHODS; WEB-BASED REPRESENTATION;

GENES;

ARTICLE; BIOCHEMISTRY; CLINICAL FEATURE; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENE MUTATION; GENETIC DIFFERENCE; GENETIC VARIABILITY; GENOMICS; KNOWLEDGE BASE; LINKAGE ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SEMANTICS; TRANSCRIPTOMICS; WEB BROWSER;

ALGORITHMS; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOMICS; HUMANS; INTERNET; KNOWLEDGE BASES; LINKAGE (GENETICS); NATURAL LANGUAGE PROCESSING; NEURAL NETWORKS (COMPUTER); QUANTITATIVE TRAIT LOCI; SEMANTICS; SOFTWARE; SYSTEMS BIOLOGY; SYSTEMS INTEGRATION;

EID: 52949136965     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2008.07.004     Document Type: Article

References (76)

1. Giallourakis C., et al. Disease gene discovery through integrative genomics. Annu Rev Genomics Hum Genet 6 (2005) 381-406
2. Tiffin N., et al. Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res 33 5 (2005) 1544-1552
3. van Driel M.A., et al. A new web-based data mining tool for the identification of candidate genes for human genetic disorders. Eur J Hum Genet 11 1 (2003) 57-63
4. Chen J., et al. Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics 8 1 (2007) 392
5. Aerts S., et al. Gene prioritization through genomic data fusion. Nat Biotechnol 24 5 (2006) 537-544
6. Turner F.S., Clutterbuck D.R., and Semple C.A. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol 4 11 (2003) R75
7. Adie E.A., et al. Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics 6 (2005) 55
8. Perez-Iratxeta C., et al. G2D: a tool for mining genes associated with disease. BMC Genet 6 (2005) 45
9. Rossi S., et al. TOM: a web-based integrated approach for identification of candidate disease genes. Nucleic Acids Res 34 Web Server issue (2006) W285-W292
10. Adie E.A., et al. SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics 22 6 (2006) 773-774
11. Freudenberg J., and Propping P. A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics 18 Suppl. 2 (2002) S110-S115
12. Lage K., et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 25 3 (2007) 309-316
13. Masseroli M., Galati O., and Pinciroli F. GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res 33 Web Server issue (2005) W717-W723
14. Gaulton K.J., Mohlke K.L., and Vision T.J. A computational system to select candidate genes for complex human traits. Bioinformatics 23 9 (2007) 1132-1140
15. English S.B., and Butte A.J. Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. Bioinformatics 23 21 (2007) 2910-2917
16. Calvo S., et al. Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet 38 5 (2006) 576-582
17. Perez-Iratxeta C., Bork P., and Andrade M.A. Association of genes to genetically inherited diseases using data mining. Nat Genet 31 3 (2002) 316-319
18. Tim Berners-Lee J.H., and Ora L. The Semantic Web. Sci Am Mag 284 (2001) 29-37
19. Available from: http://en.wikipedia.org/wiki/Eigenvector_centrality#eigenvector_centrality.
20. Junker B.H., Koschutzki D., and Schreiber F. Exploration of biological network centralities with CentiBiN. BMC Bioinformatics 7 (2006) 219
21. Bhuvan B., and Sougata M. Utilizing resource importance for ranking Semantic Web query results. Semantic Web Databases (2005) 185-198
22. Kleinberg J.M. Authoritative sources in a hyperlinked environment. J ACM 46 5 (1999) 604-632
23. Page S.B.a.L. The anatomy of a large-scale hypertextual {Web} search engine. Comput Netw ISDN Syst 30 1-7 (1998) 107-117
24. Sougata M., Bhuvan B., and Pankaj K. Information retrieval and knowledge discovery utilizing a biomedical patent Semantic Web. IEEE Educ Act Dep (2005) 1099-1110
25. Prioritizer. Available from: http://humgen.med.uu.nl/~lude/prioritizer/.
26. Liu Y., et al. An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PLoS Comput Biol 2 11 (2006) e159
27. Song L., et al. Novel locus for an inherited cardiomyopathy maps to chromosome 7. Circulation 113 18 (2006) 2186-2192
28. Ellinor P.T., et al. A novel locus for dilated cardiomyopathy, diffuse myocardial fibrosis, and sudden death on chromosome 10q25-26. J Am Coll Cardiol 48 1 (2006) 106-111
29. Grzeskowiak R., et al. Expression profiling of human idiopathic dilated cardiomyopathy. Cardiovasc Res 59 2 (2003) 400-411
30. Harris M.A., et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32 Database issue (2004) D258-D261
31. Kanehisa M., et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34 Database issue (2006) D354-D357
32. Karp P.D., et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33 19 (2005) 6083-6089
33. Joshi-Tope G., et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33 Database issue (2005) D428-D432
34. Smith C.L., Goldsmith C.A., and Eppig J.T. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6 1 (2005) R7
35. Hamosh A., et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33 Database issue (2005) D514-D517
36. Jablonski S. Jablonski's dictionary of syndromes & eponymic diseases. 2nd ed. (1991), Krieger Publication
37. Aronson A.R. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp (2001) 17-21
38. Butte A.J., and Kohane I.S. Creation and implications of a phenome-genome network. Nat Biotechnol 24 1 (2006) 55-62
39. Cunningham H. GATE, a general architecture for text engineering. Comput Humanit 36 Number 2 (2002) 223-254
40. Louie B., et al. Data integration and genomic medicine. J Biomed Inform 40 1 (2007) 5-16
41. Qu XA et al. Semantic Web-based data representation and reasoning applied to disease mechanism and pharmacology. In: Second IEEE international workshop on data mining in bioinformatics (DMB 2007). Silicon Valley, USA; 2007.
42. Rubin D.L., Noy N.F., and Musen M.A. Protege: a tool for managing and using terminology in radiology applications. J Digit Imaging 20 Suppl. 1 (2007) 34-46
43. Noy N.F., et al. Protege-2000: an open-source ontology-development and knowledge-acquisition environment. AMIA Annu Symp Proc (2003) 953
44. Mukherjea .S. Information retrieval and knowledge discovery utilising a biomedical Semantic Web. Brief Bioinform 6 3 (2005) 252-262
45. Available from: http://www.w3.org/TR/rdf-sparql-query/#construct.
46. Ohazama A., and Sharpe P.T. TFII-I gene family during tooth development: candidate genes for tooth anomalies in Williams syndrome. Dev Dyn 236 10 (2007) 2884-2888
47. van Hagen J.M., et al. Contribution of CYLN2 and GTF2IRD1 to neurological and cognitive symptoms in Williams Syndrome. Neurobiol Dis 26 1 (2007) 112-124
48. Palmer S.J., et al. Expression of Gtf2ird1, the Williams syndrome-associated gene, during mouse development. Gene Expr Patterns 7 4 (2007) 396-404
49. Edelmann L., et al. An atypical deletion of the Williams-Beuren syndrome interval implicates genes associated with defective visuospatial processing and autism. J Med Genet 44 2 (2007) 136-143
50. Hinsley T.A., et al. Comparison of TFII-I gene family members deleted in Williams-Beuren syndrome. Protein Sci 13 10 (2004) 2588-2599
51. Casanelles Mdel C., et al. Portal hypertension in Williams syndrome: report of two patients. Am J Med Genet A 118 4 (2003) 372-376
52. Piontkivska H., et al. Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions. BMC Genomics 5 1 (2004) 31
53. Tassabehji M., and Urban Z. Congenital heart disease: molecular diagnostics of supravalvular aortic stenosis. Methods Mol Med 126 (2006) 129-156
54. Hoogenraad C.C., et al. LIMK1 and CLIP-115: linking cytoskeletal defects to Williams syndrome. Bioessays 26 2 (2004) 141-150
55. Morris C.A., et al. GTF2I hemizygosity implicated in mental retardation in Williams syndrome: genotype-phenotype analysis of five families with deletions in the Williams syndrome region. Am J Med Genet A 123 1 (2003) 45-59
56. Pankau R., et al. Familial Williams-Beuren syndrome showing varying clinical expression. Am J Med Genet 98 4 (2001) 324-329
57. Cavellan E., et al. The WSTF-SNF2h chromatin remodeling complex interacts with several nuclear proteins in transcription. J Biol Chem 281 24 (2006) 16264-16271
58. Kitagawa H., et al. The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome. Cell 113 7 (2003) 905-917
59. Poot R.A., et al. Chromatin remodeling by WSTF-ISWI at the replication site: opening a window of opportunity for epigenetic inheritance?. Cell Cycle 4 4 (2005) 543-546
60. Bruno E., et al. Cardiovascular findings, and clinical course, in patients with Williams syndrome. Cardiol Young 13 6 (2003) 532-536
61. Lavine K.J., et al. Endocardial and epicardial derived FGF signals regulate myocardial proliferation and differentiation in vivo. Dev Cell 8 1 (2005) 85-95
62. Dzimiri N., et al. Differential functional expression of human myocardial G protein receptor kinases in left ventricular cardiac diseases. Eur J Pharmacol 489 3 (2004) 167-177
63. Jahns R., et al. Direct evidence for a beta 1-adrenergic receptor-directed autoimmune attack as a cause of idiopathic dilated cardiomyopathy. J Clin Invest 113 10 (2004) 1419-1429
64. Stork S., et al. Stimulating autoantibodies directed against the cardiac beta1-adrenergic receptor predict increased mortality in idiopathic cardiomyopathy. Am Heart J 152 4 (2006) 697-704
65. Archacki S.R., and Wang Q.K. Microarray analysis of cardiovascular diseases. Methods Mol Med 129 (2006) 1-13
66. Jefferies J.L., et al. Genetic predictors and remodeling of dilated cardiomyopathy in muscular dystrophy. Circulation 112 18 (2005) 2799-2804
67. Inagaki N., et al. Alpha B-crystallin mutation in dilated cardiomyopathy. Biochem Biophys Res Commun 342 2 (2006) 379-386
68. Kolcz J., et al. The expression of connexin 43 in children with Tetralogy of Fallot. Cell Mol Biol Lett 10 2 (2005) 287-303
69. Kannankeril P.J., et al. Mice with the R176Q cardiac ryanodine receptor mutation exhibit catecholamine-induced ventricular tachycardia and cardiomyopathy. Proc Natl Acad Sci USA 103 32 (2006) 12179-12184
70. Jona I., and Nanasi P.P. Cardiomyopathies and sudden cardiac death caused by RyR2 mutations: are the channels the beginning and the end?. Cardiovasc Res 71 3 (2006) 416-418
71. Clarke A.R. Murine genetic models of human disease. Curr Opin Genet Dev 4 3 (1994) 453-460
72. Goh C.S., et al. Integration of curated databases to identify genotype-phenotype associations. BMC Genomics 7 (2006) 257
73. Cantor M.N., and Lussier Y.A. Mining OMIM for insight into complex diseases. Medinfo 11 Pt 2 (2004) 753-757
74. Blake J.A., and Bult C.J. Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform 39 3 (2006) 314-320
75. Sioutos N., et al. NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform 40 1 (2007) 30-43
76. Osborne J.D., et al. Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods Mol Biol 408 (2007) 153-169