Knowledge-based computational search for genes associated with the metabolic syndrome

Bioinformatics

Volumn 21, Issue 14, 2005, Pages 3146-3154

  Matsunaga, Tsutomu ^a   Muramatsu, Masa Aki ^b,c  

^a NTT DATA Corporation   (Japan)

^b TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^c HuBit Genomix Inc   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DIABETES MELLITUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; HYPERTENSION; HYPERTRIGLYCERIDEMIA; INFORMATION RETRIEVAL; LEARNING; MACHINE; MATHEMATICAL COMPUTING; MEDICAL RESEARCH; MEDLINE; METABOLIC SYNDROME X; MOLECULAR PHYLOGENY; OBESITY; PRIORITY JOURNAL; VALIDATION PROCESS; ALGORITHM; ARTIFICIAL INTELLIGENCE; DOCUMENTATION; EVALUATION; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION; GENETICS; LINGUISTICS; METABOLISM; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PUBLICATION;

BIOLOGICAL MARKER;

ABSTRACTING AND INDEXING; ALGORITHMS; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MARKERS; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MEDLINE; METABOLIC SYNDROME X; NATURAL LANGUAGE PROCESSING; PERIODICALS; VOCABULARY, CONTROLLED;

EID: 25144441025     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti484     Document Type: Article

References (46)

1. Abusamieh,M. and Ash,J. (2004) Atherosclerosis and systemic lupus erythematosus. Cardiol Rev., 12, 267-275.
2. Ashburner,M. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
3. Bairoch,A. and Apweiler,R. (1997) The SWISS-PROT protein sequence database: Its relevance to human molecular medical research. J. Mol. Med., 75, 312-316.
4. Barabasi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nat. Rec. Genet., 5, 101-113.
5. Baxevanis,A.D. (2003) The molecular biology database collection: 2003 update. Nucleic Acids Res., 31, 1-12.
6. Bhakdi,S. et al. (1999) Complement and atherogenesis: Binding of CRP to degraded, nonoxidized LDL enhances complement activation. Arterioscler. Thromb. Vasc. Biol., 19, 2348-2354.
7. Brown,M.S. and Goldstein,J.L. (1983) Lipoprotein metabolism in the macrophage: Implications for cholesterol deposition in atherosclerosis. Ann. Rev. Biochem., 52, 223-226.
8. Collins,F.S. and Mckusick,V.A. (2001) Implications of the Human Genome Project for medical science. JAMA, 285, 540-544.
9. De Fronzo,R.A. and Ferrannini,E. (1991) Insulin resistance syndrome. A multifaceted syndrome responsible for NIDDM, obesity, hypertension, dyslipidemia, and atherosclerotic cardiovascular disease. Diabetes Care, 14, 173-194.
10. Fujioka,S. et al. (1987) Contribution of intro-abdominal fat accumulation to the impairment of glucose and lipid metabolism in human obesity. Metabolism, 36, 54-59.
11. Gregory,J. and Strausberg,R. (2001) Genome and genetic resources from the cancer genome anatomy project. Hum. Mol. Genet., 10, 663-667.
12. Halushka,M.K. et al. (1999) GIST: A web tool for collecting gene information. Physiol. Genomics, 1, 75-81.
13. Hamosh,A. et al. (2000) Online Mendelian Inheritance in Man (OMIM). Hum. Mutat., 15, 57-61.
14. Hansson,G.K. (2001) Immune mechanisms in atherosclerosis. Arterioscler. Thromb. Vasc. Biol., 21, 1876-1890.
15. Homayouni,R. et al. (2005) Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics, 21, 104-115.
16. Jenssen,T.K. et al. (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28 21-28.
17. Kannel,W.B. et al. (1971) Serum cholesterol, lipoproteins, and the risk of coronary heart disease. The Framingham study. Ann. Intern. Med., 74, 1-12.
18. Kaplan,N.M. (1989) The deadly quartet. Upper-body obesity, glucose intolerance, hypertriglyceridemia, and hypertension. Arch. Intern. Med., 149, 1514-1520.
19. Kitahara,O. et al. (2001) Alternations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissues and normal epithelia. Cancer Res., 61, 3544-3549.
20. Kobayashi,K. et al. (2003) Circulating oxidized LDL forms complexes with B2-glycoprotein I: Implication as an atherogenic autoantigen. J. Lipid Res., 44, 716-726.
21. Kodama,T. et al. (1990) Type I macrophage scavenger receptor contains alpha-helical and collagen-like coiled coils. Nature, 343, 531-535.
22. Kruglyak,L. (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet., 22, 139-144.
23. Kruskal,J.B. and Wish,M. (1978) Multidimensional scaling. Sage Publications, Beverly Hills, California.
24. Kullback,S. (1959) Information theory and statistics. John Wiley & Sons, New York.
25. Libby,P. (2002) Inflammation in atherosclerosis. Nature, 420 868-874.
26. Matsunaga,T. (2000) A study of document filtering using the subspace method of pattern recognition. Syst. Comput. Jpn, 31, 48-58.
27. Matsunaga,T. (2004) A method of knowledge modeling and its application to gene function analysis. Syst. Comput. Jpn, 35, 21-30.
28. Matsunaga,T. (2005) Disease-related gene search by association analysis based on link structure. Syst. Comput. Jpn, in press.
29. National cholesterol Education Program (2001) Executive summary of the Third Report of the National Cholesterol Education Program (NCEP) expert panel on detection, evaluation, and treatment of high blood cholesterol in adults (Adult Treatment Panel III). JAMA, 285, 2486-2497.
30. Oja,E. (1983) Subspace methods of pattern recognition. Research Studies Press Ltd, England.
31. Perez-Iratxeta,C. et al. (2002) Association of genes to genetically inherited diseases using data mining. Nat. Genet., 31, 316-319.
32. Reaven,G.M. (1988) Role of insulin resistance in human disease. Diabetes, 37, 1595-1607.
33. Rebhan,M. et al. (1998) GeneCards: A novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics, 14, 656-664.
34. Ross,R. and Glomset,J.A. (1973) Atherosclerosis and the arterial smooth muscle cell: Proliferation of smooth muscle is a key event in the genesis of the lesions of atherosclerosis. Science, 180, 1332-1339.
35. Salton,G. and Yang,C.S. (1973) On the specification of term values in automatic indexing. J. Doc., 29, 351-372.
36. Steinberg,D. et al. (1989) Beyond cholesterol. Modifications of low-density lipoprotein that increase its atherogenicity. N. Engl. J. Med., 320, 915-924.
37. Stephens,M. et al. (2001) Detecting gene relations from Medline abstracts. Pac. Symp. Biocomput., 483-495.
38. Torzewski,M. et al. (1997) Immunohistochemical colocalization of the terminal complex of human complement and smooth muscle cell alpha-actin in early atherosclerotic lesions. Arterioscler. Thromb. Vasc. Biol., 17, 2448-2452.
39. Wheeler,D.L. et al. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res., 31, 28-33.
40. Wjst,M. and Immervoll,T. (1998) An internet linkage and mutation database for the complex phenotype asthma. Bioinformatics, 14 827-828.
41. Yagi,T. et al. (2003) Identification of a gene expression signature associated with pediatric AML prognosis. Blood, 102 1849-1856.
42. Yamada,Y. et al. (2002) Prediction of the risk of myocardial infarction from polymorphisms in candidate genes. N. Engl. J. Med. 347, 1916-1923.
43. Yamaguchi,O., Fukui,K. and Maeda,K. (1998) Face recognition using temporal image sequence. In Proceedings of the third IEEE International Conference on Automatic Face and Gesture Recognition, Nara, Japan, vol. 10, pp. 318-323.
44. Zee,R.Y. et al. (2004) Polymorphism in the P-selectin and interleukin-4 genes as determinants of stroke: A population based, prospective genetic analysis. Hum. Mol. Genet., 13, 389-396.
45. Zhang,W. et al. (1997) Aggregated low density lipoprotein induces and enters surface-connected compartments of human monocyte-macrophages. Uptake occurs independently of the low density lipoprotein receptor. J. Biol. Chem., 272, 31700-31706.
46. Zhou,M. et al. (2004) VSD: A database for schizophrenia candidate genes focusing on variations. Hum. Mutat., 23, 1-7.