Complexity of type 2 diabetes mellitus data sets emerging from nutrigenomic research: A case for dimensionality reduction?

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 622, Issue 1-2, 2007, Pages 19-32

  Kaput, Jim ^a,b,c   Dawson, Kevin ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c NuGO ^*  (Netherlands)

Author keywords

Gene nutrient interactions; Nutrigenomics; Pharmacogenomics; Type 2 diabetes mellitus

Indexed keywords

ARTICLE; ARTIFICIAL NEURAL NETWORK; CHROMOSOME STRUCTURE; CHRONIC DISEASE; DATA ANALYSIS; DIABETES MELLITUS; DISEASE ASSOCIATION; DNA METHYLATION; ENVIRONMENTAL FACTOR; FACTORIAL ANALYSIS; FOOD INTAKE; GENETIC DRIFT; GENETIC POLYMORPHISM; HUMAN; NON INSULIN DEPENDENT DIABETES MELLITUS; NUTRIENT; NUTRIGENOMICS; PHARMACOGENOMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

DIABETES MELLITUS, TYPE 2; DIET; EATING; ENERGY INTAKE; GENETIC PREDISPOSITION TO DISEASE; GENOMICS; HUMANS; NUTRITION PHYSIOLOGY;

EID: 34547671411     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2007.02.033     Document Type: Article

References (176)

1. Hansen L., and Pedersen O. Genetics of type 2 diabetes mellitus: status and perspectives. Diabetes Obestest. Metab. 7 (2005) 122-135
2. Schulze M.B., and Hu F.B. Primary prevention of diabetes: what can be done and how much can be prevented?. Annu. Rev. Public Health 26 (2005) 445-467
3. Stumvoll M., Goldstein B.J., and van Haeften T.W. Type 2 diabetes: principles of pathogenesis and therapy. Lancet 365 (2005) 1333-1346
4. Kaput J., Noble J., Hatipoglu B., Kohrs K., Dawson K.k., and Bartholomew A. Application of nutrigenomic concepts to type 2 diabetes mellitus. Nutr. Metab. Cardiovasc. Dis. 17 (2007) 89-103
5. Fairweather-Tait S.J. Human nutrition and food research: opportunities and challenges in the post-genomic era. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 (2003) 1709-1727
6. Curtis J., and Wilson C. Preventing type 2 diabetes mellitus. J. Am. Board Fam. Pract. 18 (2005) 37-43
7. Pirola L., Johnston A.M., and Van Obberghen E. Modulation of insulin action. Diabetologia 47 (2004) 170-184
8. Patti M.E. Gene expression in humans with diabetes and prediabetes: what have we learned about diabetes pathophysiology?. Curr. Opin. Clin. Nutr. Metab. Care 7 (2004) 383-390
9. Parikh H., and Groop L. Candidate genes for type 2 diabetes. Rev. Endocr. Metab. Disord. 5 (2004) 151-176
10. Laakso M. Gene variants, insulin resistance, and dyslipidaemia. Curr. Opin. Lipidol. 15 (2004) 115-120
11. Steinmetz A. Treatment of diabetic dyslipoproteinemia. Exp. Clin. Endocrinol. Diabetes 111 (2003) 239-245
12. Hanson R.L., and Knowler W.C. Quantitative trait linkage studies of diabetes-related traits. Curr. Diab. Rep. 3 (2003) 176-183
13. Hansen L. Candidate genes and late-onset type 2 diabetes mellitus. Susceptibility genes or common polymorphisms?. Dan. Med. Bull. 50 (2003) 320-346
14. Florez J.C., Hirschhorn J., and Altshuler D. The inherited basis of diabetes mellitus: implications for the genetic analysis of complex traits. Annu. Rev. Genomics Hum. Genet. 4 (2003) 257-291
15. McCarthy M.I., and Froguel P. Genetic approaches to the molecular understanding of type 2 diabetes. Am. J. Physiol. Endocrinol. Metab. 283 (2002) E217-E225
16. Freeman H., and Cox R.D. Type-2 diabetes: a cocktail of genetic discovery. Hum. Mol. Genet. 15 Suppl. 2 (2006) R202-R209
17. EndocrineWeb (accessed January 31, 2006).
18. Nathan D.M. Clinical practice. Initial management of glycemia in type 2 diabetes mellitus. N. Engl. J. Med. 347 (2002) 1342-1349
19. Ahmann A.J., and Riddle M.C. Current oral agents for type 2 diabetes. Many options, but which to choose when?. Postgrad. Med. 111 (2002) (pp. 32-34, 37-40, 43-36)
20. Cordain L., Eades M.R., and Eades M.D. Hyperinsulinemic diseases of civilization: more than just syndrome X. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 136 (2003) 95-112
21. McMillen I.C., and Robinson J.S. Developmental origins of the metabolic syndrome: prediction, plasticity, and programming. Physiol. Rev. 85 (2005) 571-633
22. Koro C.E., Bowlin S.J., Bourgeois N., and Fedder D.O. Glycemic control from 1988 to 2000 among U.S. adults diagnosed with type 2 diabetes: a preliminary report. Diabetes Care 27 (2004) 17-20
23. Wolford J.K., and Vozarova de B. Courten genetic basis of type 2 diabetes mellitus: implications for therapy. Treat. Endocrinol. 3 (2004) 257-267
24. Lander E., and Kruglyak L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results [see comments]. Nat. Genet. 11 (1995) 241-247
25. Belknap J.K., Phillips T.J., and O'Toole L.A. Quantitative trait loci associated with brain weight in the BXD/Ty recombinant inbred mouse strains. Brain Res. Bull. 29 (1992) 337-344
26. Barton N.H., and Keightley P.D. Understanding quantitative genetic variation. Nat. Rev. Genet. 3 (2002) 11-21
27. Flint J., Valdar W., Shifman S., and Mott R. Strategies for mapping and cloning quantitative trait genes in rodents. Nat. Rev. Genet. 6 (2005) 271-286
28. Kaput J., Klein K.G., Reyes E.J., Kibbe W.A., Cooney C.A., Jovanovic B., Visek W.J., and Wolff G.L. Identification of genes contributing to the obese yellow Avy phenotype: caloric restriction, genotype, diet × genotype interactions. Physiol. Genomics 18 (2004) 316-324
29. Kaput J. Diet-disease gene interactions. Nutrition 20 (2004) 26-31
30. Kaput J., Swartz D., Paisley E., Mangian H., Daniel W.L., and Visek W.J. Diet-disease interactions at the molecular level: an experimental paradigm. J. Nutr. 124 (1994) 1296S-1305S
31. Seeley R.J., Drazen D.L., and Clegg D.J. The critical role of the melanocortin system in the control of energy balance. Annu. Rev. Nutr. 24 (2004) 133-149
32. Irwin M. Effects of sleep and sleep loss on immunity and cytokines. Brain Behav. Immun. 16 (2002) 503-512
33. Redwine L., Hauger R.L., Gillin J.C., and Irwin M. Effects of sleep and sleep deprivation on interleukin-6, growth hormone, cortisol, and melatonin levels in humans. J. Clin. Endocrinol. Metab. 85 (2000) 3597-3603
34. Nieman D.C., Davis J.M., Henson D.A., Walberg-Rankin J., Shute M., Dumke C.L., Utter A.C., Vinci D.M., Carson J.A., Brown A., Lee W.J., McAnulty S.R., and McAnulty L.S. Carbohydrate ingestion influences skeletal muscle cytokine mRNA and plasma cytokine levels after a 3-h run. J. Appl. Physiol. 94 (2003) 1917-1925
35. Nieman D.C., Davis J.M., Brown V.A., Henson D.A., Dumke C.L., Utter A.C., Vinci D.M., Downs M.F., Smith J.C., Carson J., Brown A., McAnulty S.R., and McAnulty L.S. Influence of carbohydrate ingestion on immune changes after 2 h of intensive resistance training. J. Appl. Physiol. 96 (2004) 1292-1298
36. Nieman D.C., Dumke C.I., Henson D.A., McAnulty S.R., McAnulty L.S., Lind R.H., and Morrow J.D. Immune and oxidative changes during and following the western states endurance run. Int. J. Sports Med. 24 (2003) 541-547
37. Chakravarthy M.V., and Booth F.W. Eating, exercise, and "thrifty" genotypes: connecting the dots toward an evolutionary understanding of modern chronic diseases. J. Appl. Physiol. 96 (2004) 3-10
38. Gleeson M., Nieman D.C., and Pedersen B.K. Exercise, nutrition and immune function. J. Sports Sci. 22 (2004) 115-125
39. Tomita M., Irwin K.I., Xie Z.J., and Santoro T.J. Tea pigments inhibit the production of type 1 (T(H1)) and type 2 (T(H2)) helper T cell cytokines in CD4(+) T cells. Phytother. Res. 16 (2002) 36-42
40. Irwin M., Clark C., Kennedy B., Christian Gillin J., and Ziegler M. Nocturnal catecholamines and immune function in insomniacs, depressed patients, and control subjects. Brain Behav. Immun. 17 (2003) 365-372
41. Ioannidis J.P. Why most published research findings are false. PLoS Med. 2 (2005) e124
42. He L., and Hannon G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5 (2004) 522-531
43. Nakahara K., and Carthew R.W. Expanding roles for miRNAs and siRNAs in cell regulation. Curr. Opin. Cell. Biol. 16 (2004) 127-133
44. Scherr M., and Eder M. RNAi in functional genomics. Curr. Opin. Mol. Ther. 6 (2004) 129-135
45. Goto A., Blandin S., Royet J., Reichhart J.M., and Levashina E.A. Silencing of Toll pathway components by direct injection of double-stranded RNA into Drosophila adult flies. Nucleic Acids Res. 31 (2003) 6619-6623
46. Caporaso N.E. Why have we failed to find the low penetrance genetic constituents of common cancers?. Cancer Epidemiol. Biomarkers Prev. 11 (2002) 1544-1549
47. Hartman J.L., Garvik B., and Hartwell L. Principles for the buffering of genetic variation. Science 291 (2001) 1001-1004
48. Yang W.S., Hsiung C.A., Ho L.T., Chen Y.T., He C.T., Curb J.D., Grove J., Quertermous T., Chen Y.D., Kuo S.S., and Chuang L.M. Genetic epistasis of adiponectin and PPARgamma2 genotypes in modulation of insulin sensitivity: a family-based association study. Diabetologia 46 (2003) 977-983
49. Jorde L.B., and Wooding S.P. Genetic variation, classification and 'race'. Nat. Genet. 36 Suppl. 1 (2004) S28-S33
50. Tishkoff S.A., and Kidd K.K. Implications of biogeography of human populations for 'race' and medicine. Nat. Genet. 36 Suppl. 1 (2004) S21-S27
51. Helgadottir A., Manolescu A., Helgason A., Thorleifsson G., Thorsteinsdottir U., Gudbjartsson D.F., Gretarsdottir S., Magnusson K.P., Gudmundsson G., Hicks A., Jonsson T., Grant S.F., Sainz J., O'Brien J., Sveinbjornsdottir S.S., Valdimarsson E.M., Matthiasson S.E., Levey A.I., Abramson J.L., Reilly M.P., Vaccarino V., Wolfe M.L., Gudnason V., Quyyumi A.A., Topol E.J., Rader D.J., Thorgeirsson G., Gulcher J.R., Hakonarson H., Kong A., and Stefansson K. A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction. Nat. Genet. 38 (2006) 68-74
52. Hamon S.C., Kardia S.L., Boerwinkle E., Liu K., Klos K.L., Clark A.G., and Sing C.F. Evidence for consistent intragenic and intergenic interactions between SNP effects in the APOA1/C3/A4/A5 gene cluster. Hum. Hered. 61 (2006) 87-96
53. D. Corella, C.Q. Lai, S. Demissie, L.A. Cupples, A.K. Manning, K.L. Tucker, J.M. Ordovas, APOA5 gene variation modulates the effects of dietary fat intake on body mass index and obesity risk in the Framingham Heart Study, J. Mol. Med., 2007.
54. Corella D., and Ordovas J.M. Single nucleotide polymorphisms that influence lipid metabolism: interaction with dietary factors. Annu. Rev. Nutr. 25 (2005) 341-390
55. Delaval K., and Feil R. Epigenetic regulation of mammalian genomic imprinting. Curr. Opin. Genet. Dev. 14 (2004) 188-195
56. Sneider T.W. Methylation of mammalian deoxyribonucleic acid. II. The distribution of 5-methylcytosine in pyrimidine deoxyribonucleotide clusters in Novikoff hepatoma cell deoxyribonucleic acid. J. Biol. Chem. 246 (1971) 4774-4783
57. Esteller M. CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene 21 (2002) 5427-5440
58. Prokhortchouk E., and Hendrich B. Methyl-CpG binding proteins and cancer: are MeCpGs more important than MBDs?. Oncogene 21 (2002) 5394-5399
59. Cho K.S., Elizondo L.I., and Boerkoel C.F. Advances in chromatin remodeling and human disease. Curr. Opin. Genet. Dev. 14 (2004) 308-315
60. Go V.L., Butrum R.R., and Wong D.A. Diet, nutrition, and cancer prevention: the postgenomic era. J. Nutr. 133 (2003) 3830S-3836S
61. Cooney C.A., Dave A.A., and Wolff G.L. Maternal methyl supplements in mice affect epigenetic variation and DNA methylation of offspring. J. Nutr. 132 (2002) 2393S-2400S
62. Mason J.B. Biomarkers of nutrient exposure and status in one-carbon (methyl) metabolism. J. Nutr. 133 Suppl. 3 (2003) 941S-947S
63. Stover P.J., and Garza C. Bringing individuality to public health recommendations. J. Nutr. 132 (2002) 2476S-2480S
64. Blander G., and Guarente L. The Sir2 family of protein deacetylases. Annu. Rev. Biochem. 73 (2004) 417-435
65. Magbanua M.J.M., Dawson K., Huang L., Malyj W., Gregg J., Galvez A., and Rodriguez R.L. Nutrient-gene interactions involving soy peptide and chemopreventive genes in prostate epithelial cells. In: Kaput J., and Rodriguez R.L. (Eds). Nutritional Genomics. Discovering the Path to Personalized Nutrition (2006), John Wiley and Sons, Hoboken, NJ 255-276
66. Young V.R., and Scrimshaw N.S. Genetic and biological variability in human nutrient requirements. Am. J. Clin. Nutr. 32 (1979) 486-500
67. Ottman R. Gene-environment interaction: definitions and study designs. Prev. Med. 25 (1996) 764-770
68. Corella D., and Ordovas J.M. The metabolic syndrome: a crossroad for genotype-phenotype associations in atherosclerosis. Curr. Atheroscler. Rep. 6 (2004) 186-196
69. Memisoglu A., Hu F.B., Hankinson S.E., Manson J.E., De Vivo I., Willett W.C., and Hunter D.J. Interaction between a peroxisome proliferator-activated receptor gamma gene polymorphism and dietary fat intake in relation to body mass. Hum. Mol. Genet. 12 (2003) 2923-2929
70. Roche H.M., Phillips C., and Gibney M.J. The metabolic syndrome: the crossroads of diet and genetics. Proc. Nutr. Soc. 64 (2005) 371-377
71. Roche H.M. Fatty acids and the metabolic syndrome. Proc. Nutr. Soc. 64 (2005) 23-29
72. Dawson K., Rodrigueez R.L., Hawkes W.C., and Malyj W. Biocomputation and the analysis of complex data sets in nutritional genomics. In: Kaput J., and Rodriguez R.L. (Eds). Nutritional Genomics. Discovering the Path to Personalized Nutrition (2006), John Wiley and Sons, Hoboken, NJ 375-402
73. Sebastiani P., Gussoni E., Kohan I.S., and Ramoni M.F. Statistical challenges in functional genomics. Stat. Sci. 18 (2003) 33-70
74. Motsinger A.A., and Ritchie M.D. Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies. Hum. Genomics 2 (2006) 318-328
75. Ritchie M.D. Bioinformatics approaches for detecting gene-gene and gene-environment interactions in studies of human disease. Neurosurg. Focus 19 (2005) E2
76. van Ommen B. Nutrigenomics: exploiting systems biology in the nutrition and health arenas. Nutrition 20 (2004) 4-8
77. West M., Ginsburg G.S., Huang A.T., and Nevins J.R. Embracing the complexity of genomic data for personalized medicine. Genome Res. 16 (2006) 559-566
78. Feitosa M.F., Province M.A., Heiss G., Arnett D.K., Myers R.H., Pankow J.S., Hopkins P.N., and Borecki I.B. Evidence of QTL on 15q21 for high-density lipoprotein cholesterol: The National Heart, Lung, and Blood Institute Family Heart Study (NHLBI FHS). Atherosclerosis 190 (2007) 232-237
79. Wilke R.A., Reif D.M., and Moore J.H. Combinatorial pharmacogenetics. Nat. Rev. Drug Discov. 4 (2005) 911-918
80. Dawson K., Rodriguez R.L., and Malyj W. Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm. BMC Bioinform. 6 (2005) 195
81. Williams S.M., Ritchie M.D., Phillips III J.A., Dawson E., Prince M., Dzhura E., Willis A., Semenya A., Summar M., White B.C., Addy J.H., Kpodonu J., Wong L.J., Felder R.A., Jose P.A., and Moore J.H. Multilocus analysis of hypertension: a hierarchical approach. Hum. Hered. 57 (2004) 28-38
82. Moore J.H. Computational analysis of gene-gene interactions using multifactor dimensionality reduction. Expert Rev. Mol. Diagn. 4 (2004) 795-803
83. Cho Y.M., Ritchie M.D., Moore J.H., Park J.Y., Lee K.U., Shin H.D., Lee H.K., and Park K.S. Multifactor-dimensionality reduction shows a two-locus interaction associated with type 2 diabetes mellitus. Diabetologia 47 (2004) 549-554
84. Bastone L., Reilly M., Rader D.J., and Foulkes A.S. MDR and PRP: a comparison of methods for high-order genotype-phenotype associations. Hum. Hered. 58 (2004) 82-92
85. Lan H., Stoehr J.P., Nadler S.T., Schueler K.L., Yandell B.S., and Attie A.D. Dimension reduction for mapping mRNA abundance as quantitative traits. Genetics 164 (2003) 1607-1614
86. Wang J., Delabie J., Aasheim H., Smeland E., and Myklebost O. Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinform. 3 (2002) 36
87. Barroso I., Luan J., Middelberg R.P., Harding A.H., Franks P.W., Jakes R.W., Clayton D., Schafer A.J., O'Rahilly S., and Wareham N.J. Candidate gene association study in type 2 diabetes indicates a role for genes involved in beta-cell function as well as insulin action. PLoS Biol. 1 (2003) E20
88. Hani E.H., Clement K., Velho G., Vionnet N., Hager J., Philippi A., Dina C., Inoue H., Permutt M.A., Basdevant A., North M., Demenais F., Guy-Grand B., and Froguel P. Genetic studies of the sulfonylurea receptor gene locus in NIDDM and in morbid obesity among French Caucasians. Diabetes 46 (1997) 688-694
89. Lucarini N., Antonacci E., Bottini N., Borgiani P., Faggioni G., and Gloria-Bottini F. Phosphotyrosine-protein-phosphatase and diabetic disorders.Further studies on the relationship between low molecular weight acid phosphatase genotype and degree of glycemic control. Dis. Markers 14 (1998) 121-125
90. Bottini E., and Gloria-Bottini F. Adenosine deaminase and body mass index in non-insulin-dependent diabetes mellitus. Metabolism 48 (1999) 949-951
91. Gonzalez Sanchez J.L., Proenza A.M., Martinez Larrad M.T., Ramis J.M., Fernandez Perez C., Palou A., and Serrano Rios M. The glutamine 27 glutamic acid polymorphism of the beta2-adrenoceptor gene is associated with abdominal obesity and greater risk of impaired glucose tolerance in men but not in women: a population-based study in Spain. Clin. Endocrinol. (Oxf.) 59 (2003) 476-481
92. Ellsworth D.L., Coady S.A., Chen W., Srinivasan S.R., Elkasabany A., Gustat J., Boerwinkle E., and Berenson G.S. Influence of the beta2-adrenergic receptor Arg16Gly polymorphism on longitudinal changes in obesity from childhood through young adulthood in a biracial cohort: the Bogalusa Heart Study. Int. J. Obestet. Relat. Metab. Disord. 26 (2002) 928-937
93. Barroso I. Genetics of type 2 diabetes. Diabetes Med. 22 (2005) 517-535
94. Marks D.L., Boucher N., Lanouette C.M., Perusse L., Brookhart G., Comuzzie A.G., Chagnon Y.C., and Cone R.D. Ala67Thr polymorphism in the agouti-related peptide gene is associated with inherited leanness in humans. Am. J. Med. Genet. A 126 (2004) 267-271
95. Fumeron F., Aubert R., Siddiq A., Betoulle D., Pean F., Hadjadj S., Tichet J., Wilpart E., Chesnier M.C., Balkau B., Froguel P., and Marre M. Adiponectin gene polymorphisms and adiponectin levels are independently associated with the development of hyperglycemia during a 3-year period: the epidemiologic data on the insulin resistance syndrome prospective study. Diabetes 53 (2004) 1150-1157
96. Gu H.F., Abulaiti A., Ostenson C.G., Humphreys K., Wahlestedt C., Brookes A.J., and Efendic S. Single nucleotide polymorphisms in the proximal promoter region of the adiponectin (APM1) gene are associated with type 2 diabetes in Swedish caucasians. Diabetes 53 Suppl. 1 (2004) S31-S35
97. Leipold H., Knofler M., Gruber C., Haslinger P., Bancher-Todesca D., and Worda C. Calpain-10 haplotype combination and association with gestational diabetes mellitus. Obstet. Gynecol. 103 (2004) 1235-1240
98. Carlsson E., Fredriksson J., Groop L., and Ridderstrale M. Variation in the calpain-10 gene is associated with elevated triglyceride levels and reduced adipose tissue messenger ribonucleic acid expression in obese Swedish subjects. J. Clin. Endocrinol. Metab. 89 (2004) 3601-3605
99. Hamaguchi K., Terao H., Kusuda Y., Yamashita T., Hazoury Bahles J.A., Cruz L.M., Brugal V.L., Jongchong W.B., Yoshimatsu H., and Sakata T. The PC-1 Q121 allele is exceptionally prevalent in the Dominican Republic and is associated with type 2 diabetes. J. Clin. Endocrinol. Metab. 89 (2004) 1359-1364
100. Weiss E.P., Brown M.D., Shuldiner A.R., and Hagberg J.M. Fatty acid binding protein-2 gene variants and insulin resistance: gene and gene-environment interaction effects. Physiol. Genomics 10 (2002) 145-157
101. Gertow K., Bellanda M., Eriksson P., Boquist S., Hamsten A., Sunnerhagen M., and Fisher R.M. Genetic and structural evaluation of fatty acid transport protein-4 in relation to markers of the insulin resistance syndrome. J. Clin. Endocrinol. Metab. 89 (2004) 392-399
102. Carlsson E., Groop L., and Ridderstrale M. Role of the FOXC2-512C > T polymorphism in type 2 diabetes: possible association with the dysmetabolic syndrome. Int. J. Obestet. Relat. Metab. Disord. 29 (2005) 268-274
103. Holmkvist J., Almgren P., Parikh H., Zucchelli M., Kere J., Groop L., and Lindgren C.M. Haplotype construction of the FRDA gene and evaluation of its role in type II diabetes. Eur. J. Hum. Genet. 13 (2005) 849-855
104. Hirai M., Suzuki S., Hinokio Y., Hirai A., Chiba M., Akai H., Suzuki C., and Toyota T. Variations in vitamin D-binding protein (group-specific component protein) are associated with fasting plasma insulin levels in Japanese with normal glucose tolerance. J. Clin. Endocrinol. Metab. 85 (2000) 1951-1953
105. Marz W., Nauck M., Hoffmann M.M., Nagel D., Boehm B.O., Koenig W., Rothenbacher D., and Winkelmann B.R. G(-30)A polymorphism in the pancreatic promoter of the glucokinase gene associated with angiographic coronary artery disease and type 2 diabetes mellitus. Circulation 109 (2004) 2844-2849
106. Gidh-Jain M., Takeda J., Xu L.Z., Lange A.J., Vionnet N., Stoffel M., Froguel P., Velho G., Sun F., and Cohen D. Glucokinase mutations associated with non-insulin-dependent (type 2) diabetes mellitus have decreased enzymatic activity: implications for structure/function relationships. Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 1932-1936
107. Takeda J., Gidh-Jain M., Xu L.Z., Froguel P., Velho G., Vaxillaire M., Cohen D., Shimada F., Makino H., Nishi S., et al. Structure/function studies of human beta-cell glucokinase. Enzymatic properties of a sequence polymorphism, mutations associated with diabetes, and other site-directed mutants. J. Biol. Chem. 268 (1993) 15200-15204
108. Zhang H., Jia Y., Cooper J.J., Hale T., Zhang Z., and Elbein S.C. Common variants in glutamine:fructose-6-phosphate amidotransferase 2 (GFPT2) gene are associated with type 2 diabetes, diabetic nephropathy, and increased GFPT2 mRNA levels. J. Clin. Endocrinol. Metab. 89 (2004) 748-755
109. Miraglia del Giudice E., Santoro N., Cirillo G., Raimondo P., Grandone A., D'Aniello A., Di Nardo M., and Perrone L. Molecular screening of the ghrelin gene in Italian obese children: the Leu72Met variant is associated with an earlier onset of obesity. Int. J. Obestet. Relat. Metab. Disord. 28 (2004) 447-450
110. Korbonits M., Gueorguiev M., O'Grady E., Lecoeur C., Swan D.C., Mein C.A., Weill J., Grossman A.B., and Froguel P. A variation in the ghrelin gene increases weight and decreases insulin secretion in tall, obese children. J. Clin. Endocrinol. Metab. 87 (2002) 4005-4008
111. Poston W.S., Haddock C.K., Spertus J., Catanese D.M., Pavlik V.N., Hyman D.J., Hanis C.L., and Forevt J.P. Physical activity does not mitigate G-protein-related genetic risk for obesity in individuals of African descent. Eat Weight Disord. 7 (2002) 68-71
112. Boutin P., Gresh L., Cisse A., Hara M., Bell G., Babu S., Eisenbarth G., and Froguel P. Missense mutation Gly574Ser in the transcription factor HNF-1alpha is a marker of atypical diabetes mellitus in African-American children. Diabetologia 42 (1999) 380-381
113. Gasa R., Gomis R., Casamitjana R., Rivera F., and Novials A. Glucose regulation of islet amyloid polypeptide gene expression in rat pancreatic islets. Am. J. Physiol. 272 (1997) E543-E549
114. Ritzel R.A., and Butler P.C. Replication increases beta-cell vulnerability to human islet amyloid polypeptide-induced apoptosis. Diabetes 52 (2003) 1701-1708
115. Arends N., Johnston L., Hokken-Koelega A., van Duijn C., de Ridder M., Savage M., and Clark A. Polymorphism in the IGF-I gene: clinical relevance for short children born small for gestational age (SGA). J. Clin. Endocrinol. Metab. 87 (2002) 2720
116. Mohlig M., Boeing H., Spranger J., Osterhoff M., Kroke A., Fisher E., Bergmann M.M., Ristow M., Hoffmann K., and Pfeiffer A.F. Body mass index and C-174G interleukin-6 promoter polymorphism interact in predicting type 2 diabetes. J. Clin. Endocrinol. Metab. 89 (2004) 1885-1890
117. McKenzie J.A., Weiss E.P., Ghiu I.A., Kulaputana O., Phares D.A., Ferrell R.E., and Hagberg J.M. Influence of the interleukin-6-174 G/C gene polymorphism on exercise training-induced changes in glucose tolerance indexes. J. Appl. Physiol. 97 (2004) 1338-1342
118. Kubaszek A., Pihlajamaki J., Komarovski V., Lindi V., Lindstrom J., Eriksson J., Valle T.T., Hamalainen H., Ilanne-Parikka P., Keinanen-Kiukaanniemi S., Tuomilehto J., Uusitupa M., and Laakso M. Promoter polymorphisms of the TNF-alpha (G-308A) and IL-6 (C-174G) genes predict the conversion from impaired glucose tolerance to type 2 diabetes: the Finnish Diabetes Prevention Study. Diabetes 52 (2003) 1872-1876
119. Hassan M.I., Aschner Y., Manning C.H., Xu J., and Aschner J.L. Racial differences in selected cytokine allelic and genotypic frequencies among healthy, pregnant women in North Carolina. Cytokine 21 (2003) 10-16
120. Sanchez-Corona J., Flores-Martinez S.E., Machorro-Lazo M.V., Galaviz-Hernandez C., Moran-Moguel M.C., Perea F.J., Mujica-Lopez K.I., Vargas-Ancona L., Laviada-Molina H.A., Fernandez V., Pardio J., Arroyo P., Barrera H., and Hanson R.L. Polymorphisms in candidate genes for type 2 diabetes mellitus in a Mexican population with metabolic syndrome findings. Diabetes Res. Clin. Pract. 63 (2004) 47-55
121. Undlien D.E., Bennett S.T., Todd J.A., Akselsen H.E., Ikaheimo I., Reijonen H., Knip M., Thorsby E., and Ronningen K.S. Insulin gene region-encoded susceptibility to IDDM maps upstream of the insulin gene. Diabetes 44 (1995) 620-625
122. Matejkova-Behanova M., Vankova M., Hill M., Kucera P., Cinek O., Andel M., and Bendlova B. Polymorphism of INS VNTR is associated with glutamic acid decarboxylase antibodies and postprandial C-peptide in patients with onset of diabetes after 35 years of age. Physiol. Res. 53 (2004) 187-190
123. Heude B., Dubois S., Charles M.A., Deweirder M., Dina C., Borys J.M., Ducimetiere P., and Froguel P. VNTR polymorphism of the insulin gene and childhood overweight in a general population. Obestet. Res. 12 (2004) 499-504
124. Macfarlane W.M., Frayling T.M., Ellard S., Evans J.C., Allen L.I., Bulman M.P., Ayres S., Shepherd M., Clark P., Millward A., Demaine A., Wilkin T., Docherty K., and Hattersley A.T. Missense mutations in the insulin promoter factor-1 gene predispose to type 2 diabetes. J. Clin. Invest. 104 (1999) R33-R39
125. Hani E.H., Stoffers D.A., Chevre J.C., Durand E., Stanojevic V., Dina C., Habener J.F., and Froguel P. Defective mutations in the insulin promoter factor-1 (IPF-1) gene in late-onset type 2 diabetes mellitus. J. Clin. Invest. 104 (1999) R41-R48
126. Yamada K., Yuan X., Ishiyama S., Ichikawa F., Kohno S., Shoji S., Hayashi H., and Nonaka K. Identification of a single nucleotide insertion polymorphism in the upstream region of the insulin promoter factor-1 gene: an association study with diabetes mellitus. Diabetologia 41 (1998) 603-605
127. Mammarella S., Romano F., Di Valerio A., Creati B., Esposito D.L., Palmirotta R., Capani F., Vitullo P., Volpe G., Battista P., Della Loggia F., Mariani-Costantini R., and Cama A. Interaction between the G1057D variant of IRS-2 and overweight in the pathogenesis of type 2 diabetes. Hum. Mol. Genet. 9 (2000) 2517-2521
128. Nielsen E.M., Hansen L., Carstensen B., Echwald S.M., Drivsholm T., Glumer C., Thorsteinsson B., Borch-Johnsen K., Hansen T., and Pedersen O. The E23K variant of Kir6.2 associates with impaired post-OGTT serum insulin response and increased risk of type 2 diabetes. Diabetes 52 (2003) 573-577
129. Todorova B., Kubaszek A., Pihlajamaki J., Lindstrom J., Eriksson J., Valle T.T., Hamalainen H., Ilanne-Parikka P., Keinanen-Kiukaanniemi S., Tuomilehto J., Uusitupa M., and Laakso M. The G-250A promoter polymorphism of the hepatic lipase gene predicts the conversion from impaired glucose tolerance to type 2 diabetes mellitus: the Finnish Diabetes Prevention Study. J. Clin. Endocrinol. Metab. 89 (2004) 2019-2023
130. Yabu Y., Noma K., Nakatani K., Nishioka J., Suematsu M., Katsuki A., Hori Y., Yano Y., Sumida Y., Wada H., and Nobori T. C-514T polymorphism in hepatic lipase gene promoter is associated with elevated triglyceride levels and decreasing insulin sensitivity in nondiabetic Japanese subjects. Int. J. Mol. Med. 16 (2005) 421-425
131. Ma Y.Q., Thomas G.N., Ng M.C., Critchley J.A., Chan J.C., and Tomlinson B. The lipoprotein lipase gene HindIII polymorphism is associated with lipid levels in early-onset type 2 diabetic patients. Metabolism 52 (2003) 338-343
132. Malecki M.T., Jhala U.S., Antonellis A., Fields L., Doria A., Orban T., Saad M., Warram J.H., Montminy M., and Krolewski A.S. Mutations in NEUROD1 are associated with the development of type 2 diabetes mellitus. Nat. Genet. 23 (1999) 323-328
133. Ruiz-Quezada S., Vazquez-Del Mercado M., Parra-Rojas I., Rangel-Villalobos H., Best-Aguilera C., Sanchez-Orozco L.V., and Munoz-Valle J.F. Genotype and allele frequency of PAI-1 promoter polymorphism in healthy subjects from the west of Mexico. Association with biochemical and hematological parameters. Ann. Genet. 47 (2004) 155-162
134. Lopes C., Dina C., Durand E., and Froguel P. PAI-1 polymorphisms modulate phenotypes associated with the metabolic syndrome in obese and diabetic Caucasian population. Diabetologia 46 (2003) 1284-1290
135. Hoffstedt J., Andersson I.L., Persson L., Isaksson B., and Arner P. The common -675 4G/5G polymorphism in the plasminogen activator inhibitor -1 gene is strongly associated with obesity. Diabetologia 45 (2002) 584-587
136. Cao H., van der Veer E., Ban M.R., Hanley A.J., Zinman B., Harris S.B., Young T.K., Pickering J.G., and Hegele R.A. Promoter polymorphism in PCK1 (phosphoenolpyruvate carboxykinase gene) associated with type 2 diabetes mellitus. J. Clin. Endocrinol. Metab. 89 (2004) 898-903
137. Muller Y.L., Bogardus C., Pedersen O., and Baier L. A Gly482Ser missense mutation in the peroxisome proliferator-activated receptor gamma coactivator-1 is associated with altered lipid oxidation and early insulin secretion in Pima Indians. Diabetes 52 (2003) 895-898
138. Hara K., Tobe K., Okada T., Kadowaki H., Akanuma Y., Ito C., Kimura S., and Kadowaki T. A genetic variation in the PGC-1 gene could confer insulin resistance and susceptibility to Type II diabetes. Diabetologia 45 (2002) 740-743
139. Ek J., Andersen G., Urhammer S.A., Gaede P.H., Drivsholm T., Borch-Johnsen K., Hansen T., and Pedersen O. Mutation analysis of peroxisome proliferator-activated receptor-gamma coactivator-1 (PGC-1) and relationships of identified amino acid polymorphisms to type II diabetes mellitus. Diabetologia 44 (2001) 2220-2226
140. Hansen L., Zethelius B., Berglund L., Reneland R., Hansen T., Berne C., Lithell H., Hemmings B.A., and Pedersen O. In vitro and in vivo studies of a naturally occurring variant of the human p85alpha regulatory subunit of the phosphoinositide 3-kinase: inhibition of protein kinase B and relationships with type 2 diabetes, insulin secretion, glucose disappearance constant, and insulin sensitivity. Diabetes 50 (2001) 690-693
141. Fanella S., Harris S.B., Young T.K., Hanley A.J., Zinman B., Connelly P.W., and Hegele R.A. Association between PON1 L/M55 polymorphism and plasma lipoproteins in two Canadian aboriginal populations. Clin. Chem. Lab. Med. 38 (2000) 413-420
142. Kao W.H., Coresh J., Shuldiner A.R., Boerwinkle E., Bray M.S., and Brancati F.L. Pro12Ala of the peroxisome proliferator-activated receptor-gamma2 gene is associated with lower serum insulin levels in nonobese African Americans: the Atherosclerosis Risk in Communities Study. Diabetes 52 (2003) 1568-1572
143. Doney A., Fischer B., Frew D., Cumming A., Flavell D.M., World M., Montgomery H.E., Boyle D., Morris A., and Palmer C.N. Haplotype analysis of the PPARgamma Pro12Ala and C1431T variants reveals opposing associations with body weight. BMC Genet. 3 (2002) 21
144. Doney A.S., Fischer B., Cecil J.E., Boylan K., McGuigan F.E., Ralston S.H., Morris A.D., and Palmer C.N. Association of the Pro12Ala and C1431T variants of PPARG and their haplotypes with susceptibility to type 2 diabetes. Diabetologia 47 (2004) 555-558
145. Permana P.A., and Mott D.M. Genetic analysis of human type 1 protein phosphatase inhibitor 2 in insulin-resistant Pima Indians. Genomics 41 (1997) 110-114
146. Xia J., Scherer S.W., Cohen P.T., Majer M., Xi T., Norman R.A., Knowler W.C., Bogardus C., and Prochazka M. A common variant in PPP1R3 associated with insulin resistance and type 2 diabetes. Diabetes 47 (1998) 1519-1524
147. Wang H., Chu W., Das S.K., Zheng Z., Hasstedt S.J., and Elbein S.C. Molecular screening and association studies of retinoid-related orphan receptor gamma (RORC): a positional and functional candidate for type 2 diabetes. Mol. Genet. Metab. 79 (2003) 176-182
148. Garvey W.T., Maianu L., Kennedy A., Wallace P., Ganaway E., Hamacher L.L., Yarnall D.P., Lenhard J.M., and Burns D.K. Muscle Rad expression and human metabolism: potential role of the novel Ras-related GTPase in energy expenditure and body composition. Diabetes 46 (1997) 444-450
149. S.F. Grant, G. Thorleifsson, I. Reynisdottir, R. Benediktsson, A. Manolescu, J. Sainz, A. Helgason, H. Stefansson, V. Emilsson, A. Helgadottir, U. Styrkarsdottir, K.P. Magnusson, G.B. Walters, E. Palsdottir, T. Jonsdottir, T. Gudmundsdottir, A. Gylfason, J. Saemundsdottir, R.L. Wilensky, M.P. Reilly, D.J. Rader, Y. Bagger, C. Christiansen, V. Gudnason, G. Sigurdsson, U. Thorsteinsdottir, J.R. Gulcher, A. Kong, K. Stefansson, Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes, Nat. Genet., 2006.
150. Sesti G., Cardellini M., Marini M.A., Frontoni S., D'Adamo M., Del Guerra S., Lauro D., De Nicolais P., Sbraccia P., Del Prato S., Gambardella S., Federici M., Marchetti P., and Lauro R. A common polymorphism in the promoter of ucp2 contributes to the variation in insulin secretion in glucose-tolerant subjects. Diabetes 52 (2003) 1280-1283
151. Le Fur S., Le Stunff C., Dos Santos C., and Bougneres P. The common -866 G/A polymorphism in the promoter of uncoupling protein 2 is associated with increased carbohydrate and decreased lipid oxidation in juvenile obesity. Diabetes 53 (2004) 235-239
152. D'Adamo M., Perego L., Cardellini M., Marini M.A., Frontoni S., Andreozzi F., Sciacqua A., Lauro D., Sbraccia P., Federici M., Paganelli M., Pontiroli A.E., Lauro R., Perticone F., Folli F., and Sesti G. The -866A/A genotype in the promoter of the human uncoupling protein 2 gene is associated with insulin resistance and increased risk of type 2 diabetes. Diabetes 53 (2004) 1905-1910
153. Mantzoros C.S., Williams C.J., Manson J.E., Meigs J.B., and Hu F.B. Adherence to the Mediterranean dietary pattern is positively associated with plasma adiponectin concentrations in diabetic women. Am. J. Clin. Nutr. 84 (2006) 328-335
154. Cardillo S., Seshadri P., and Iqbal N. The effects of a low-carbohydrate versus low-fat diet on adipocytokines in severely obese adults: three-year follow-up of a randomized trial. Eur. Rev. Med. Pharmacol. Sci. 10 (2006) 99-106
155. Butte N.F., Comuzzie A.G., Cai G., Cole S.A., Mehta N.R., and Bacino C.A. Genetic and environmental factors influencing fasting serum adiponectin in Hispanic children. J. Clin. Endocrinol. Metab. 90 (2005) 4170-4176
156. Eisenach J.H., Schroeder D.R., Pike T.L., Johnson C.P., Schrage W.G., Snyder E.M., Johnson B.D., Garovic V.D., Turner S.T., and Joyner M.J. Dietary sodium restriction and beta2-adrenergic receptor polymorphism modulate cardiovascular function in humans. J. Physiol. 574 (2006) 955-965
157. Loos R.J., Rankinen T., Rice T., Rao D.C., Leon A.S., Skinner J.S., Bouchard C., and Argyropoulos G. Two ethnic-specific polymorphisms in the human agouti-related protein gene are associated with macronutrient intake. Am. J. Clin. Nutr. 82 (2005) 1097-1101
158. Tozawa Y. G protein beta3 subunit variant: tendency of increasing susceptibility to hypertension in Japanese. Blood Press 10 (2001) 131-134
159. Bos G., Dekker J.M., Feskens E.J., Ocke M.C., Nijpels G., Stehouwer C.D., Bouter L.M., Heine R.J., and Jansen H. Interactions of dietary fat intake and the hepatic lipase -480C->T polymorphism in determining hepatic lipase activity: the Hoorn Study. Am. J. Clin. Nutr. 81 (2005) 911-915
160. Dos Santos C., Fallin D., Le Stunff C., LeFur S., and Bougneres P. INS VNTR is a QTL for the insulin response to oral glucose in obese children. Physiol. Genomics 16 (2004) 309-313
161. Sierksma A., van der Gaag M.S., van Tol A., James R.W., and Hendriks H.F. Kinetics of HDL cholesterol and paraoxonase activity in moderate alcohol consumers. Alcohol Clin. Exp. Res. 26 (2002) 1430-1435
162. Cha M.H., Shin H.D., Kim K.S., Lee B.H., and Yoon Y. The effects of uncoupling protein 3 haplotypes on obesity phenotypes and very low-energy diet-induced changes among overweight Korean female subjects. Metabolism 55 (2006) 578-586
163. Ukkola O., Tremblay A., Sun G., Chagnon Y.C., and Bouchard C. Genetic variation at the uncoupling protein 1, 2 and 3 loci and the response to long-term overfeeding. Eur. J. Clin. Nutr. 55 (2001) 1008-1015
164. Kustra R., Shioda R., and Zhu M. A factor analysis model for functional genomics. BMC Bioinform. 7 (2006) 216
165. Taguchi Y.H., and Oono Y. Relational patterns of gene expression via non-metric multidimensional scaling analysis. Bioinformatics 21 (2005) 730-740
166. Tan Y., Shi L., Tong W., and Wang C. Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data. Nucleic Acids Res. 33 (2005) 56-65
167. Liu L., Hawkins D.M., Ghosh S., and Young S.S. Robust singular value decomposition analysis of microarray data. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 13167-13172
168. Niyogi M.B.P. Laplacian eigenmaps for dimensionality reduction and data representation. Neural Computat. 15 (2003) 1373-1396
169. Roweis S.T., and Saul L.K. Nonlinear dimensionality reduction by locally linear embedding. Science 290 (2000) 2323-2326
170. Tenenbaum J.B., de Silva V., and Langford J.C. A global geometric framework for nonlinear dimensionality reduction. Science 290 (2000) 2319-2323
171. Donoho D.L., and Grimes C. Hessian eigenmaps: locally linear embedding techniques for high-dimensional data. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 5591-5596
172. Mendez M.A., Hodar C., Vulpe C., Gonzalez M., and Cambiazo V. Discriminant analysis to evaluate clustering of gene expression data. FEBS Lett. 522 (2002) 24-28
173. Papana A., and Ishwaran H. CART variance stabilization and regularization for high-throughput genomic data. Bioinformatics 22 (2006) 2254-2261
174. Beiko R.G., and Charlebois R.L. GANN: genetic algorithm neural networks for the detection of conserved combinations of features in DNA. BMC Bioinform. 6 (2005) 36
175. Yang Z.R. Biological applications of support vector machines. Brief Bioinform. 5 (2004) 328-338
176. Jimenez-Sanchez G., Childs B., and Valle D. Human disease genes. Nature 409 (2001) 853-855