publication . Article . 2009

Gene hunting of the Genetic Analysis Workshop 16 rheumatoid arthritis data using rough set theory

Aporntewan Chatchawit; Ballard David H; Lee Ji; Lee Joon; Wu Zheyang; Zhao Hongyu;
Open Access English
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3, issue Suppl 7, pages S126-S126 (eissn: 1753-6561, Copyright policy)
  • Publisher: BioMed Central
Abstract
<p>Abstract</p> <p>We propose to use the rough set theory to identify genes affecting rheumatoid arthritis risk from the data collected by the North American Rheumatoid Arthritis Consortium. For each gene, we employ generalized dynamic reducts in the rough set theory to select a subset of single-nucleotide polymorphisms (SNPs) to represent the genetic information from this gene. We then group the study subjects into different clusters based on their genotype similarity at the selected markers. Statistical association between disease status and cluster membership is then studied to identify genes associated with rheumatoid arthritis. Based on our proposed approac...
Subjects
free text keywords: Proceedings, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Medicine, Medicine, business.industry, business, Genetic predisposition, Genetic analysis, Gene, Rheumatoid factor, PTPN22, Single-nucleotide polymorphism, Rheumatoid arthritis, medicine.disease, Computational biology, Genotype, Bioinformatics
Funded by
NIH| Biomedical Informatics and Data Science Training at Yale
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T15LM007056-32
  • Funding stream: NATIONAL LIBRARY OF MEDICINE
,
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
WT
Project
  • Funder: Wellcome Trust (WT)
,
NIH| Thai-US Drug Dependence Genetics Research Training Grant
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5D43TW006166-03
  • Funding stream: FOGARTY INTERNATIONAL CENTER
24 references, page 1 of 2

Orozco, G, Rueda, B, Martin, J. Genetic basis of rheumatoid arthritis. Biomed Pharmacother. 2006; 60: 656-662 [PubMed]

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007; 447: 661-678 [OpenAIRE] [PubMed]

Plenge, RM, Cotsapas, C, Davies, L, Price, AL, de Bakker, PI, Maller, J, Pe'er, I, Burtt, NP, Blumenstiel, B, DeFelice, M, Parkin, M, Barry, R, Winslow, W, Healy, C, Graham, RR, Neale, BM, Izmailova, E, Roubenoff, R, Parker, AN, Glass, R, Karlson, EW, Maher, N, Hafler, DA, Lee, DM, Seldin, MF, Remmers, EF, Lee, AT, Padyukov, L, Alfredsson, L, Coblyn, J, Weinblatt, ME, Gabriel, SB, Purcell, S, Klareskog, L, Gregersen, PK, Shadick, NA, Daly, MJ, Altshuler, D. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet. 2007; 39: 1477-1482 [OpenAIRE] [PubMed]

Remmers, EF, Plenge, RM, Lee, AT, Graham, RR, Hom, G, Behrens, TW, de Bakker, PI, Le, JM, Lee, HS, Batliwalla, F, Li, W, Masters, SL, Booty, MG, Carulli, JP, Padyukov, L, Alfredsson, L, Klareskog, L, Chen, WV, Amos, CI, Criswell, LA, Seldin, MF, Kastner, DL, Gregersen, PK. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med. 2007; 357: 977-986 [OpenAIRE] [PubMed]

Plenge, RM, Seielstad, M, Padyukov, L, Lee, AT, Remmers, EF, Ding, B, Liew, A, Khalili, H, Chandrasekaran, A, Davies, LR, Li, W, Tan, AK, Bonnard, C, Ong, RT, Thalamuthu, A, Pettersson, S, Liu, C, Tian, C, Chen, WV, Carulli, JP, Beckman, EM, Altshuler, D, Alfredsson, L, Criswell, LA, Amos, CI, Seldin, MF, Kastner, DL, Klareskog, L, Gregersen, PK. TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med. 2007; 357: 1199-1209 [OpenAIRE] [PubMed]

Neale, BM, Sham, PC. The future of association studies: gene-based analysis and replication. Am J Hum Genet. 2004; 75: 353-362 [OpenAIRE] [PubMed]

Polkowski, L. Rough Sets: Mathematical Foundations. 2002

Wei, L, Huang, C, Chen, C. Data mining of the GAW14 simulated data using rough set theory and tree-based methods. BMC Genet. 2005; 6 (suppl 1): S133 [OpenAIRE] [PubMed]

Bazan, JG, Szczuka, S, Wróblewski, J. A new version of rough set exploration system. Rough Sets and Current Trends in Computing, LNCS 2475. 2002: 397-404 [OpenAIRE]

Berkhin, P. Survey of clustering data mining techniques.

Dunn, J. Well separated clusters and optimal fuzzy partitions. J Cybernetics. 1974; 4: 95-104

Kraskov, A, Stögbauer, H, Andrzejak, RG, Grassberger, P. Hierarchical clustering based on mutual information.

Perera, A, Buil, A, Di Bernardo, MC, Sabater-Lleal, M, Pattini, L, Souto, JC, Fontcuberta, J, Vallverdu, M, Soria, JM, Caminal, P. Clustering of individuals given SNPs similarity based on normalized mutual information: F7 SNPs in the GAIT sample. Conf Proc IEEE Eng Med Biol Soc. 2007; 2007: 123-126 [OpenAIRE] [PubMed]

Gao, X, Starmer, J. Human population structure detection via multi-locus genotype clustering. BMC Genet. 2007; 8: 1471-2156 [OpenAIRE]

Irigoyen, P, Lee, AT, Wener, MH, Li, W, Kern, M, Batliwalla, F, Lum, RF, Massarotti, E, Weisman, M, Bombardier, C, Remmers, EF, Kastner, DL, Seldin, MF, Criswell, LA, Gregersen, PK. Regulation of anti-cyclic citrullinated peptide antibodies in rheumatoid arthritis: contrasting effects of HLA-DR3 and the shared epitope alleles. Arthritis Rheum. 2005; 52: 3813-3818 [PubMed]

24 references, page 1 of 2
Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue