Genome-wide gene and pathway analysis

European Journal of Human Genetics

Volumn 18, Issue 9, 2010, Pages 1045-1053

  Luo, Li ^a   Peng, Gang ^a   Zhu, Yun ^b   Dong, Hua ^a,b   Amos, Christopher I ^c   Xiong, Momiao ^a  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^b FUDAN UNIVERSITY   (China)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

complex diseases; gene association analysis; GWAS; pathway association analysis

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; CONTROLLED STUDY; GENE REPLICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77955981355     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2010.62     Document Type: Article

References (42)

1. Zhernakova A, van Diemen CC, Wijmenga C: Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet 2009; 10: 43-55.
2. Schadt EE, Lum PY: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes. J Lipid Res 2006; 47: 2601-2613.
3. Manolio TA, Collins FS, Cox NJ et al: Finding the missing heritability of complex diseases. Nature 2009; 461: 747-753.
4. Neale BM, Sham PC: The future of association studies: gene-based analysis and replication. Am J Hum Genet 2004; 75: 353-362.
5. Olden K, Wilson S: Environmental health and genomics: visions and implications. Nat Rev Genet 2000; 1: 149-153.
6. Carlson CS, Eberle MA, Kruglyak L, Nickerson DA: Mapping complex disease loci in whole-genome association studies. Nature 2004; 429: 446-452.
7. Benfey PN, Mitchell-Olds T: From genotype to phenotype: systems biology meets natural variation. Science 2008; 320: 495-497.
8. Feldman I, Rzhetsky A, Vitkup D: Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci USA 2008; 105: 4323-4328.
9. Barabasi AL: Network medicine-from obesity to the 'diseasome'. N Engl J Med 2007; 357: 404-407.
10. Wang K, Li M, Bucan M: Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 2007; 81: 1278-1283.
11. Fisher RA: Statistical Methods for Research Workers; 4th edn: London: Oliver and Boyd 1932.
12. Pounds S, Cheng C: Robust estimation of the false discovery rate. Bioinformatics 2006; 22: 1979-1987.
13. Nothnagel M: Simulation of LD block-structured SNP haplotype data and its use for the analysis of case-control data by supervised learning methods. Am J Hum Genet 2002; 71 (Suppl): A2363.
14. 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.
15. Plenge RM, Seielstad M, Padyukov L et al: TRAF1-C5 as a risk locus for rheumatoid arthritis-a genomewide study. N Engl J Med 2007; 357: 1199-1209.
16. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999; 27: 29-34.
17. Carthy D, MacGregor A, Awomoi A et al: HLA-DPB1*0201 is associated with particular clinical features of rheumatoid arthritis. Rev Rhum Engl Ed 1995; 62: 163-168.
18. Gao X, Fernandez-Vina M, Olsen NJ, Pincus T, Stastny P: HLA-DPB1*0301 is a major risk factor for rheumatoid factor-negative adult rheumatoid arthritis. Arthritis Rheum 1991; 34: 1310-1312.
19. Hadj Kacem H, Kaddour N, Adyel FZ, Bahloul Z, Ayadi H: HLA-DQB1 CAR1/CAR2, TNFa IR2/IR4 and CTLA-4 polymorphisms in Tunisian patients with rheumatoid arthritis and Sjogren's syndrome. Rheumatology (Oxford) 2001; 40: 1370-1374.
20. Seidl C, Donner H, Petershofen E et al: An endogenous retroviral long terminal repeat at the HLA-DQB1 gene locus confers susceptibility to rheumatoid arthritis. Hum Immunol 1999; 60: 63-68.
21. Mok JW, Lee YJ, Kim JY et al: Association of MICA polymorphism with rheumatoid arthritis patients in Koreans. Hum Immunol 2003; 64: 1190-1194.
22. Singal DP, Li J, Zhang G: Microsatellite polymorphism of the MICA gene and susceptibility to rheumatoid arthritis. Clin Exp Rheumatol 2001; 19: 451-452.
23. Alkassab F, Gourh P, Tan FK et al: An allograft inflammatory factor 1 (AIF1) single nucleotide polymorphism (SNP) is associated with anticentromere antibody positive systemic sclerosis. Rheumatology (Oxford) 2007; 46: 1248-1251.
24. Arvanitis DA, Flouris GA, Spandidos DA: Genomic rearrangements on VCAM1, SELE, APEG1and AIF1 loci in atherosclerosis. J Cell Mol Med 2005; 9: 153-159.
25. Okada K, Yano M, Doki Y et al: Injection of LPS causes transient suppression of biological clock genes in rats. J Surg Res 2008; 145: 5-12.
26. Mackay DJ, Callaway JL, Marks SM et al: Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. Nat Genet 2008; 40: 949-951.
27. Yamada R, Yamamoto K: Mechanisms of disease: genetics of rheumatoid arthritis-ethnic differences in disease-associated genes. Nat Clin Pract Rheumatol 2007; 3: 644-650.
28. Kanazawa S, Ota S, Sekine C et al: Aberrant MHC class II expression in mouse joints leads to arthritis with extraarticular manifestations similar to rheumatoid arthritis. Proc Natl Acad Sci USA 2006; 103: 14465-14470.
29. Crawford JM, Watanabe K: Cell adhesion molecules in inflammation and immunity: relevance to periodontal diseases. Crit Rev Oral Biol Med 1994; 5: 91-123.
30. Vreugdenhil GR: Enteroviruses and type 1 diabetes mellitus putative pathogenic pathways. Dissertation 2001, http://hdl.handle.net/2066/19000.
31. Schett G, Zwerina J, Firestein G: The p38 mitogen-activated protein kinase (MAPK) pathway in rheumatoid arthritis. Ann Rheum Dis 2008; 67: 909-916.
32. Low JM, Moore TL: A role for the complement system in rheumatoid arthritis. Curr Pharm Des 2005; 11: 655-670.
33. Markiewski MM, Nilsson B, Ekdahl KN, Mollnes TE, Lambris JD: Complement and coagulation: strangers or partners in crime? Trends Immunol 2007; 28: 184-192.
34. van der Pouw Kraan TC, Wijbrandts CA, van Baarsen L et al: Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 2007; 66: 1008-1014.
35. Gorska MM, Cen O, Liang Q, Stafford SJ, Alam R: Differential regulation of interleukin 5-stimulated signaling pathways by dynamic. J Biol Chem 2006; 281: 14429-14439.
36. Bouros D: Sexy and 17: two novel pathways in immune regulation. Pneumon 2007; 20: 216-218.
37. Chang SK, Mihalcik SA, Jelinek DF: B lymphocyte stimulator regulates adaptive immune responses by directly promoting dendritic cell maturation. J Immunol 2008; 180: 7394-7403.
38. Kasahara T, Kato T: Nutritional biochemistry: a new redox-cofactor vitamin for mammals. Nature 2003; 422: 832.
39. Cariappa A, Pillai S: Antigen-dependent B-cell development. Curr Opin Immunol 2002; 14: 241-249.
40. Ullrich O, Schneider-Stock R, Zipp F: Cell-cell communication by endocannabinoids during immune surveillance of the central nervous system. Results Probl Cell Differ 2006; 43: 281-305.
41. Quah BJ, Barlow VP, McPhun V, Matthaei KI, Hulett MD, Parish CR: Bystander B cells rapidly acquire antigen receptors from activated B cells by membrane transfer. Proc Natl Acad Sci USA 2008; 105: 4259-4264.
42. Koukouritaki SB, Tamizuddin A, Lianos EA: Enhanced expression of the cytoskeleton-associated proteins paxillin and focal adhesion kinase in glomerular immune injury. J Lab Clin Med 1999; 134: 173-179.