Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes

BMC Systems Biology

Volumn 6, Issue SUPPL3, 2012, Pages

  Hale, Paul J ^a,b   López Yunez, Alfredo M ^c   Chen, Jake Y ^a,b,d  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c Alevio Medical Center   (United States)

^d WENZHOU MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TCF7L2 PROTEIN, HUMAN; TRANSCRIPTION FACTOR 7 LIKE 2;

ALLELE; ARTICLE; BIOLOGICAL MODEL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS; HUMAN; HUMAN CHROMOSOME; META ANALYSIS; METABOLISM; METHODOLOGY; NON INSULIN DEPENDENT DIABETES MELLITUS; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMS BIOLOGY;

ALLELES; CHROMOSOMES, HUMAN; DIABETES MELLITUS, TYPE 2; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; SYSTEMS BIOLOGY; TRANSCRIPTION FACTOR 7-LIKE 2 PROTEIN;

MLCS; MLOWN;

EID: 84878893384     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-S3-S16     Document Type: Article

References (38)

1. Wheeler E, Barroso I. Genome-wide association studies and type 2 diabetes. Brief Funct Genomics 2011, 10(2):52-60. 10.1093/bfgp/elr008, 21436302.
2. Cruz M, Valladares-Salgado A, Garcia-Mena J, Ross K, Edwards M, Angeles-Martinez J, Ortega-Camarillo C, de la Pena JE, Burguete-Garcia AI, Wacher-Rodarte N, et al. Candidate gene association study conditioning on individual ancestry in patients with type 2 diabetes and metabolic syndrome from Mexico City. Diabetes Metab Res Rev 2010, 26(4):261-270. 10.1002/dmrr.1082, 20503258.
3. Lin Y, Li P, Cai L, Zhang B, Tang X, Zhang X, Li Y, Xian Y, Yang Y, Wang L, et al. Association study of genetic variants in eight genes/loci with type 2 diabetes in a Han Chinese population. BMC Med Genet 2010, 11:97. 2894791, 20550665.
4. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, Boutin P, Vincent D, Belisle A, Hadjadj S, et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 2007, 445(7130):881-885. 10.1038/nature05616, 17293876.
5. Gaulton KJ, Willer CJ, Li Y, Scott LJ, Conneely KN, Jackson AU, Duren WL, Chines PS, Narisu N, Bonnycastle LL, et al. Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes. Diabetes 2008, 57(11):3136-3144. 10.2337/db07-1731, 2570412, 18678618.
6. Hu C, Zhang R, Wang C, Wang J, Ma X, Lu J, Qin W, Hou X, Bao Y, Xiang K, et al. PPARG, KCNJ11, CDKAL1, CDKN2A-CDKN2B, IDE-KIF11-HHEX, IGF2BP2 and SLC30A8 are associated with type 2 diabetes in a Chinese population. PLoS One 2009, 4(10):e7643. 10.1371/journal.pone.0007643, 2763267, 19862325.
7. Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, Erdos MR, Stringham HM, Chines PS, Jackson AU, et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 2007, 316(5829):1341-1345. 10.1126/science.1142382, 3214617, 17463248.
8. So HC, Gui AH, Cherny SS, Sham PC. Evaluating the heritability explained by known susceptibility variants: a survey of ten complex diseases. Genet Epidemiol 2011, 35(5):310-317. 10.1002/gepi.20579, 21374718.
9. Cauchi S, Meyre D, Durand E, Proenca C, Marre M, Hadjadj S, Choquet H, De Graeve F, Gaget S, Allegaert F, et al. Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value. PLoS One 2008, 3(5):e2031. 10.1371/journal.pone.0002031, 2346547, 18461161.
10. Sharma A, Chavali S, Tabassum R, Tandon N, Bharadwaj D. Gene prioritization in Type 2 Diabetes using domain interactions and network analysis. BMC Genomics 2010, 11:84. 10.1186/1471-2164-11-84, 2824729, 20122255.
11. Jesmin J, Rashid MS, Jamil H, Hontecillas R, Bassaganya-Riera J. Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension. BMC Med Genomics 2010, 3(1):45. 10.1186/1755-8794-3-45, 2965702, 20942928.
12. Lim JE, Hong KW, Jin HS, Kim YS, Park HK, Oh B. Type 2 diabetes genetic association database manually curated for the study design and odds ratio. BMC Med Inform Decis Mak 2010, 10:76. 10.1186/1472-6947-10-76, 3022779, 21190593.
13. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic acids research 2001, 29(1):308-311. 10.1093/nar/29.1.308, 29783, 11125122.
14. Chen JY, Mamidipalli S, Huan T. HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC genomics 2009, 10(Suppl 1):S16. 10.1186/1471-2164-10-S1-S16, 2788368, 19958479.
15. Loveland J. VEGA, the genome browser with a difference. Brief Bioinform 2005, 6(2):189-193. 10.1093/bib/6.2.189, 15975227.
16. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic acids research 2007, 35(Database):D358-362. 10.1093/nar/gkl825, 1669762, 17098935.
17. Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics 2005, 21(9):2076-2082. 10.1093/bioinformatics/bti273, 15657099.
18. 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 research 2005, 33(Database):D418-424. 540005, 15608229.
19. Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, et al. Human protein reference database--2006 update. Nucleic acids research 2006, 34(Database):D411-414. 1347503, 16381900.
20. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G. MINT: the Molecular INTeraction database. Nucleic acids research 2007, 35(Database):D572-574. 10.1093/nar/gkl950, 1751541, 17135203.
21. Li J, Zhu X, Chen JY. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol 2009, 5(7):e1000450. 10.1371/journal.pcbi.1000450, 2709445, 19649302.
22. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research 2009, 37(1):1-13. 10.1093/nar/gkn923, 2615629, 19033363.
23. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
24. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic acids research 2012, 40(Database):D109-114. 3245020, 22080510.
25. Rho K, Kim B, Jang Y, Lee S, Bae T, Seo J, Seo C, Lee J, Kang H, Yu U, et al. GARNET--gene set analysis with exploration of annotation relations. BMC Bioinformatics 2011, 12(Suppl 1):S25. 10.1186/1471-2105-12-S1-S25, 3278842, 22373185.
26. Ji L, Malecki M, Warram JH, Yang Y, Rich SS, Krolewski AS. New susceptibility locus for NIDDM is localized to human chromosome 20 q. Diabetes 1997, 46(5):876-881. 10.2337/diabetes.46.5.876, 9133558.
27. Zouali H, Hani EH, Philippi A, Vionnet N, Beckmann JS, Demenais F, Froguel P. A susceptibility locus for early-onset non-insulin dependent (type 2) diabetes mellitus maps to chromosome 20 q, proximal to the phosphoenolpyruvate carboxykinase gene. Hum Mol Genet 1997, 6(9):1401-1408. 10.1093/hmg/6.9.1401, 9285775.
28. Sandovici I, Smith NH, Nitert MD, Ackers-Johnson M, Uribe-Lewis S, Ito Y, Jones RH, Marquez VE, Cairns W, Tadayyon M, et al. Maternal diet and aging alter the epigenetic control of a promoter-enhancer interaction at the Hnf4a gene in rat pancreatic islets. Proc Natl Acad Sci USA 2011, 108(13):5449-5454. 10.1073/pnas.1019007108, 3069181, 21385945.
29. Barroso I, Luan J, Middelberg RP, Harding AH, Franks PW, Jakes RW, Clayton D, Schafer AJ, O'Rahilly S, Wareham NJ. 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 2003, 1(1):E20. 10.1371/journal.pbio.0000020, 212698, 14551916.
30. Malodobra M, Pilecka A, Gworys B, Adamiec R. Single nucleotide polymorphisms within functional regions of genes implicated in insulin action and association with the insulin resistant phenotype. Mol Cell Biochem 2011, 349(1-2):187-193. 10.1007/s11010-010-0673-5, 21113646.
31. Rasche A, Al-Hasani H, Herwig R. Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics 2008, 9:310. 10.1186/1471-2164-9-310, 2515154, 18590522.
32. Huang Q, Wang TH, Lu WS, Mu PW, Yang YF, Liang WW, Li CX, Lin GP. Estrogen receptor alpha gene polymorphism associated with type 2 diabetes mellitus and the serum lipid concentration in Chinese women in Guangzhou. Chin Med J (Engl) 2006, 119(21):1794-1801.
33. Dahlman I, Vaxillaire M, Nilsson M, Lecoeur C, Gu HF, Cavalcanti-Proenca C, Efendic S, Ostenson CG, Brismar K, Charpentier G, et al. Estrogen receptor alpha gene variants associate with type 2 diabetes and fasting plasma glucose. Pharmacogenet Genomics 2008, 18(11):967-975. 10.1097/FPC.0b013e32831101ef, 18854778.
34. Di Paola R, Caporarello N, Marucci A, Dimatteo C, Iadicicco C, Del Guerra S, Prudente S, Sudano D, Miele C, Parrino C, et al. ENPP1 affects insulin action and secretion: evidences from in vitro studies. PLoS One 2011, 6(5):e19462. 10.1371/journal.pone.0019462, 3088669, 21573217.
35. Wang J, Kuusisto J, Vanttinen M, Kuulasmaa T, Lindstrom J, Tuomilehto J, Uusitupa M, Laakso M. Variants of transcription factor 7-like 2 (TCF7L2) gene predict conversion to type 2 diabetes in the Finnish Diabetes Prevention Study and are associated with impaired glucose regulation and impaired insulin secretion. Diabetologia 2007, 50(6):1192-1200. 10.1007/s00125-007-0656-6, 17437080.
36. Horikoshi M, Hara K, Ito C, Nagai R, Froguel P, Kadowaki T. A genetic variation of the transcription factor 7-like 2 gene is associated with risk of type 2 diabetes in the Japanese population. Diabetologia 2007, 50(4):747-751. 10.1007/s00125-006-0588-6, 17245589.
37. Ren Q, Han XY, Wang F, Zhang XY, Han LC, Luo YY, Zhou XH, Ji LN. Exon sequencing and association analysis of polymorphisms in TCF7L2 with type 2 diabetes in a Chinese population. Diabetologia 2008, 51(7):1146-1152. 10.1007/s00125-008-1039-3, 18493736.
38. Guo T, Hanson RL, Traurig M, Muller YL, Ma L, Mack J, Kobes S, Knowler WC, Bogardus C, Baier LJ. TCF7L2 is not a major susceptibility gene for type 2 diabetes in Pima Indians: analysis of 3,501 individuals. Diabetes 2007, 56(12):3082-3088. 10.2337/db07-0621, 17909099.