Using biological networks to search for interacting loci in genome-wide association studies

European Journal of Human Genetics

Volumn 17, Issue 10, 2009, Pages 1231-1240

  Emily, Mathieu ^a,b   Mailund, Thomas ^a   Hein, Jotun ^c   Schauser, Leif ^a   Schierup, Mikkel Heide ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b Université Rennes 2 Haute Bretagne Campus Villejean ^*  (France)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIPOLAR DISORDER; CONTROLLED STUDY; CROHN DISEASE; EPISTASIS; GENE INTERACTION; GENE LOCUS; GENETIC SUSCEPTIBILITY; GENOME ANALYSIS; HUMAN; HYPERTENSION; PRIORITY JOURNAL; PROTEIN DATABASE; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; ARTHRITIS, RHEUMATOID; BIPOLAR DISORDER; COMPUTATIONAL BIOLOGY; CROHN DISEASE; EPISTASIS, GENETIC; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; HYPERTENSION; MODELS, GENETIC; MODELS, STATISTICAL; PHENOTYPE; PROTEIN INTERACTION MAPPING; RISK FACTORS;

EID: 70349629971     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2009.15     Document Type: Article

References (39)

1. Consortium International Human Genome Sequencing: Initial sequencing and analysis of the human genome. Nature 2001; 409: 860-921.
2. HapMap: The International HapMap Project. Nature 2003; 426: 789-796.
3. The Wellcome Trust Case Control Consortium: Genome-wide association study of 14 000 cases of seven common diseases and 3000 shared controls. Nature 2007; 447: 661-678.
4. Curtis D: Allelic association studies of genome wide association data can reveal errors in marker position assignments. BMC Genetics 2007; 8: 30.
5. Marchini J, Donnelly P, Cardon LR: Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005; 37: 413-417.
6. Evans DM, Marchini J, Morris AP, Cardon LR: Two-stage two-locus models in genome-wide association. PLoS Genet 2006; 2: E157.
7. Wang K, Li M, Bucan M: Pathway-based approaches for analysis of Genomewide Association Studies. Am J Human Genet 2007; 81: 1278-1283.
8. Pattin KA, Moore JH: Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human dieases. Human Genet 2008; 124: 19-29.
9. Von Mering C, Jensen LJ, Kuhn M et al: STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acid Res 2007; 35: D358-D362.
10. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The database of interacting proteins: 2004-pdate. Nucleic Acid Res 2004; 32: D449-D451.
11. Mishra GR, Suresh M, Kumaran K et al: Human protein reference database - 2006 update. Nucleic Acid Res 2006; 34: D411-D414.
12. Hubbard TJP, Aken BL, Beal K et al: Ensembl 2007. Nucleic Acid Res 2007; 35: D610-D617.
13. CordeWl HJ: Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Human Mol Genet 2002; 11: 2463-2468.
14. Devlin B, Bacan-S-A, Roeder K: Genomic control to the extreme. Nat Genet 2004; 36: 1129-1130.
15. Devlin B, Roeder K: Genomic control for association studies. Biometrics 1999; 55: 997-1004.
16. Li J, Ji L: Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity 2005; 95: 221-227.
17. Cover TM, Thomas JA: Elements of Information Theory. John Wiley and Sons, Inc.: New York, 1991.
18. Stirling WD: Enhancements to aid interpretation of probability plots. Statistician 1982; 31: 211-220.
19. Pickrell J, Clerget-Darpoux F, Bourgain C: Power of genome-wide association studies in the presence of interacting loci. Genet Epidemiol 2007; 31: 748-762.
20. Sharma M, Henderson BR: IQ-domain GTPase-activating protein 1 regulates beta-catenin at membrane ruffles and its role in macropinocytosis of N-cadherin and adenomatous polyposis coli. J Biol Chem 2007; 282: 8545-8556.
21. Fearnhead NS, Britton MP, Bodmer WF: The ABC of APC. Human Mol Genet 2001; 10: 721-733.
22. Huang X, Guo B: Adenomatous polyposis coli determines sensitivity to histone deacetylase inhibitor-induced apoptosis in colon cancer cells. Cancer Res 2006; 66: 9245-9251.
23. Clark EA, Golub TR, Lander ES, Hynes RO: Genomic analysis of metastasis reveals an essential role for RhoC. Nature 2000; 406: 532-535.
24. Nabeshima K, Shimao Y, Inoue T, Koono M: Immunohistochemical analysis of IQGAP1 expression in human colorectal carcinomas: Its overexpression in carcinomas and association with invasion fronts. Cancer Letts 2002; 176: 101-109.
25. Morris LE, Bloom GS, Frierson HFJ, Powell SM: Nucleotide variants within IQGAP1 gene in diffuse-type gastric cancers. Genes Chromosomes Cancer 2005; 42: 280-286.
26. De Franceschi L, Platt OS, Malpeli G et al: Protective effects of phosphodiesterase-4 (PDE-4) inhibition in the early phase of pulmonary arterial hypertension in transgenic sickle cell mice. FASEB J 2008; 22: 1849-1860.
27. DuAlio A, Faraonio R, Minopoli G, Zambrano N, Russo T: Fe65L2: a new member of the Fe65 protein family interacting with the intracellular domain of the Alzheimer's beta-amyloid precursor protein. Biochem J 1998; 330: 513-519.
28. Chang Y, Tesco G, Jeong W et al: Generation of the beta-amyloid peptide and the amyloid precursor protein C-terminal fragment gamma are potentiated by FE65L1. J Biol Chem 2003; 278: 51100-51107.
29. Brugg B, Dubreuil YL, Huber G, Wollman EE, Delhaye-Bouchaud N, Mariani J: Inflammatory processes induce beta-amyloid precursor protein changes in mouse brain. Proc Natl Acad Sci 1995; 92: 3032-3035.
30. Fukushima K, Funayama Y, Shibata C et al: Familial adenomatous polyposis complicated with Crohn's disease. Intl J Colorectal Dis 2006; 21: 730-731.
31. Ekborn A, Helmick C, Zack M, Adami H: Increased risk of large-bowel cancer in Crohn's disease with colonic involvement. Lancet 1990; 336: 357-359.
32. Shimada A, Hirato J, Kuroiwa M et al: Expression of KIT and PDGFR is associated with a good prognosis in neuroblastoma. Pediatr Blood Cancer 2008; 50: 213-217.
33. Prabakaran S, Swatton J, Ryan M et al: Mitochondrial dysfunction in schizophrenia: Evidence for compromised brain metabolism and oxidative stress. Mol Psychiatr 2004; 9: 684-697.
34. Drzyzgaa Ł, Obuchowicz E, Marcinowskaa A, Herman ZS: Cytokines in schizophrenia and the effects of antipsychotic drugs. Brain Behav Immun 2006; 20: 532-545.
35. Growcott EJ, Spink KG, Ren X, Afzal S, Banner KH, Wharton J: Phosphodiesterase type 4 expression and anti-proliferative effects in human pulmonary artery smooth muscle cells. Resp Res 2006; 7 1-12.
36. Green K, Billings L, Roozendaal B, McGaugh J, LaFerla F: Glucocorticoids increase amyloid-beta and tau pathology in a mouse model of Alzheimer's disease. J Neurosci 2006; 26: 9047-9056.
37. McGeer P, McGeer E, Rogers G, Sibley J: Anti-inflammatory drugs and Alzheimer disease. Lancet 1990; 335: 1037.
38. Myllykangas-Luosujarvi R, Isomaki H: Alzheimer's disease and rheumatoid arthritis. Brit J Rheumatol 1994; 33: 501-502.
39. McGeer P, Schulzer M, McGeer E: Arthritis and anti-inflammatory agents as possible protective factors for Alzeihmer's disease: A review of 17 epidemiologic studies. Neurology 1996; 47: 425-432.