Comparative analysis of a novel disease phenotype network based on clinical manifestations

Journal of Biomedical Informatics

Volumn 53, Issue , 2015, Pages 113-120

  Chen, Yang ^a,b   Zhang, Xiang ^a   Zhang, Guo Qiang ^a,b   Xu, Rong ^b  

^a Case Western Reserve University   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Disease phenotype network; Network analysis; Ontology

Indexed keywords

ELECTRIC NETWORK ANALYSIS; ONTOLOGY; SEMANTICS;

CLINICAL MANIFESTATION; COMPARATIVE ANALYSIS; DISEASE PHENOTYPES; FUNCTIONAL INTERACTION; GENETIC RELATIONSHIPS; PATHOPHYSIOLOGICAL; SEMANTIC RELATIONSHIPS; TEXTUAL DESCRIPTION;

CHROMOSOMES;

ARTICLE; CLINICAL FEATURE; COMMUNITY STRUCTURE; COMPARATIVE STUDY; DISEASE PHENOTYPE NETWORK; ENVIRONMENTAL FACTOR; GENETIC ASSOCIATION; GENETIC DISORDER; HUMAN; LIFESTYLE; MARFAN SYNDROME; MOLECULAR PHYLOGENY; PHENOTYPE; PRIORITY JOURNAL; ALGORITHM; BIOLOGY; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; GENOTYPE; MUTATION; PROCEDURES; REPRODUCIBILITY; STATISTICAL MODEL; UNIFIED MEDICAL LANGUAGE SYSTEM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENOTYPE; HUMANS; MARFAN SYNDROME; MODELS, STATISTICAL; MUTATION; PHENOTYPE; REPRODUCIBILITY OF RESULTS; UNIFIED MEDICAL LANGUAGE SYSTEM;

EID: 84924524532     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2014.09.007     Document Type: Article

References (49)

1. Annunen S., Körkkö J., Czarny M., Warman M.L., Brunner H.G., Kääriäinen H., et al. Splicing mutations of 54-bp exons in the col11a1 gene cause marshall syndrome, but other mutations cause overlapping marshall/stickler phenotypes. Am J Human Genet 1999, 65(4):974-983.
2. Barabási A.L., Gulbahce N., Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 2011, 12(1):56-68.
3. Bell D.S., Greenes R., Doubilet P. Form-based clinical input from a structured vocabulary: initial application in ultrasound reporting. Proceedings of the annual symposium on computer application in medical care 1992, 789. American Medical Informatics Association.
4. Bodenreider O. The unified medical language system (umls): integrating biomedical terminology. Nucl Acids Res 2004, 32(Suppl. 1):D267-D270.
5. Brunner H.G., van Driel M.A. From syndrome families to functional genomics. Nat Rev Genet 2004, 5(7):545-551.
6. Butte A.J., Kohane I.S. Creation and implications of a phenome-genome network. Nat Biotechnol 2006, 24(1):55-62.
7. Callier P., Aral B., Hanna N., Lambert S., Dindy H., Ragon C., et al. Systematic molecular and cytogenetic screening of 100 patients with marfanoid syndromes and intellectual disability. Clin Genet 2013.
8. Caretta-Cartozo C., De Los Rios P., Piazza F., Liò P. Bottleneck genes and community structure in the cell cycle network of s. pombe. PLoS Comput Biol 2007, 3(6):e103.
9. Fang H., Gough J. A disease-drug-phenotype matrix inferred by walking on a functional domain network. Mol BioSyst 2013, 9(7):1686-1696.
10. Fang H., Gough J. A domain-centric solution to functional genomics via dcgo predictor. BMC Bioinform 2013, 14(Suppl. 3):S9.
11. Fryns J.-P., Buttiens M., Opitz J.M., Reynolds J.F. X-linked mental retardation with marfanoid habitus. Am J Med Genet 1987, 28(2):267-274.
12. Goh K.-I., Cusick M.E., Valle D., Childs B., Vidal M., Barabási A.-L. The human disease network. Proc Natl Acad Sci 2007, 104(21):8685-8690.
13. Grahame R., Hakim A.J. Arachnodactyly-a key to diagnosing heritable disorders of connective tissue. Nat Rev Rheumatol 2013, 9(6):358-364.
14. 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. Nucl Acids Res 2005, 33(Suppl. 1):D514-D517.
15. Houle D., Govindaraju D.R., Omholt S. Phenomics: the next challenge. Nat Rev Genet 2010, 11(12):855-866.
16. Hwang T., Atluri G., Xie M., Dey S., Hong C., Kumar V., et al. Co-clustering phenome-genome for phenotype classification and disease gene discovery. Nucl Acids Res 2012, 40(19). e146-e146.
17. Köhler S., Bauer S., Horn D., Robinson P.N. Walking the interactome for prioritization of candidate disease genes. Am J Human Genet 2008, 82(4):949-958.
18. Korbel J.O., Doerks T., Jensen L.J., Perez-Iratxeta C., Kaczanowski S., Hooper S.D., et al. Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol 2005, 3(5):e134.
19. Lage K., Karlberg E.O., Størling Z.M., Olason P.I., Pedersen A.G., Rigina O., et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 2007, 25(3):309-316.
20. Lee Y., Li H., Li J., Rebman E., Achour I., Regan K.E., et al. Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. J Am Med Inform Assoc 2013, 20(4):619-629.
21. Lerma-Carrillo I., Molina J.D., Cuevas-Duran T., Julve-Correcher C., Espejo-Saavedra J.M., Andrade-Rosa C., et al. Psychopathology in the lujan-fryns syndrome: report of two patients and review. Am J Med Genet Part A 2006, 140(24):2807-2811.
22. Li H., Lee Y., Chen J.L., Rebman E., Li J., Lussier Y.A. Complex-disease networks of trait-associated single-nucleotide polymorphisms (snps) unveiled by information theory. J Am Med Inform Assoc 2012, 19(2):295-305.
23. Li Y., Patra J.C. Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network. Bioinformatics 2010, 26(9):1219-1224.
24. Lindberg D.A., Humphreys B.L., McCray A.T. The unified medical language system. Methods Inform Med 1993, 32(4):281-291.
25. McCray A.T. An upper-level ontology for the biomedical domain. Compar Funct Genom 2003, 4(1):80-84.
26. Mestres J., Gregori-Puigjané E., Valverde S., Sole R.V. Data completeness-the achilles heel of drug-target networks. Nat Biotechnol 2008, 26(9):983-984.
27. Murphy-Ryan M., Psychogios A., Lindor N.M. Hereditary disorders of connective tissue: a guide to the emerging differential diagnosis. Genet Med 2010, 12(6):344-354.
28. Newman M.E., Girvan M. Finding and evaluating community structure in networks. Phys Rev E 2004, 69(2):026113.
29. Oti M., Huynen M.A., Brunner H.G. Phenome connections. Trends Genet 2008, 24(3):103-106.
30. Oti M., Huynen M.A., Brunner H.G. The biological coherence of human phenome databases. Am J Human Genet 2009, 85(6):801-808.
31. Palla G., Derényi I., Farkas I., Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435(7043):814-818.
32. Piro R.M., Di Cunto F. Computational approaches to disease-gene prediction: rationale, classification and successes. FEBS J 2012, 279(5):678-696.
33. Piro R.M., Molineris I., Di Cunto F., Eils R., König R. Disease-gene discovery by integration of 3d gene expression and transcription factor binding affinities. Bioinformatics 2013, 29(4):468-475.
34. Salathé M., Jones J.H. Dynamics and control of diseases in networks with community structure. PLoS Comput Biol 2010, 6(4):e1000736.
35. Sifrim A., Popovic D., Tranchevent L.-C., Ardeshirdavani A., Sakai R., Konings P., et al. Extasy: variant prioritization by genomic data fusion. Nat Methods 2013, 10(11):1083-1084.
36. Singh-Blom U.M., Natarajan N., Tewari A., Woods J.O., Dhillon I.S., Marcotte E.M. Prediction and validation of gene-disease associations using methods inspired by social network analyses. PloS One 2013, 8(5):e58977.
37. Singleton M.V., Guthery S.L., Voelkerding K.V., Chen K., Kennedy B., Margraf R.L., et al. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Human Genet 2014, 94(4):599-610.
38. Tiffin N., Andrade-Navarro M.A., Perez-Iratxeta C. Linking genes to diseases: it's all in the data. Genome Med 2009, 1(8):77.
39. Tranchevent L.-C., Capdevila F.B., 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.
40. Tringali M., Hole W.T., Srinivasan S. Integration of a standard gastrointestinal endoscopy terminology in the umls metathesaurus. Proceedings of the AMIA symposium 2002, 801. American Medical Informatics Association.
41. Van Buggenhout G., JP F. Lujan-fryns syndrome (mental retardation, x-linked, marfanoid habitus). Orphanet J Rare Dis 2006, 1(26):325.
42. van Driel M.A., Bruggeman J., Vriend G., Brunner H.G., Leunissen J.A. A text-mining analysis of the human phenome. Eur J Human Genet 2006, 14(5):535-542.
43. 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.
44. Wang X., Gulbahce N., Yu H. Network-based methods for human disease gene prediction. Brief Funct Genom 2011, 10(5):280-293.
45. Webb G.D., Smallhorn J.F., Therrien J. Congenital heart disease. Heart disease: a textbook of cardiovascular medicine 2011, vol. 2:53-76. Saunders Elsevier. 9th ed. R.O. Bonow, D.L. Man, D.P. Zipes (Eds.).
46. Wu X., Jiang R., Zhang M.Q., Li S. Network-based global inference of human disease genes. Mol Syst Biol 2008, 4(1).
47. Wu X., Liu Q., Jiang R. Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinformatics 2009, 25(1):98-104.
48. Xu J., Li Y. Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics 2006, 22(22):2800-2805.
49. Xu R., Li L., Wang Q. Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature. Bioinformatics 2013, 29(17):2186-2194.