Prediction of SNP interactions in complex diseases with mutual information and boolean algebra

임상섭; Kyubum Wee

Journal of The Korea Society of Computer and Information

Abbr : JKSCI
2010, 15(11), pp.215-224
Publisher : The Korean Society Of Computer And Information
Research Area : Computer Science

임상섭 ¹ , Kyubum Wee ²

¹ 아주대학교
² 아주대학교

ABSTRACT

Most chronic diseases are complex diseases which are caused by interactions of several genes. Studies on finding SNPs and gene-gene interactions involved in the development of complex diseases can contribute to prevention and treatment of the diseases. Previous studies mostly concentrate on finding only the set of SNPs involved. In this study we suggest a way to see how these SNPs interact using boolean expressions. The proposed method consists of two stages. In the first stage we find the set of SNPs involved in the development of diseases using mutual information based on entropy. In the second stage we find the highest accuracy boolean expression that consists of the SNP set obtained in the first stage. We experimented with clinical data to demonstrate the effectiveness of the proposed method. We also compared the differences between our method and the previous results on the SNP associations studies.
KEYWORDS

복합질환(complex diseases) , 단일염기다형성(single nucleotide polymorphism , SNP) , 부울식(boolean expressions) , 엔트로피(entropy) , 상호정보(mutual information)
REFERENCES (24)

[journal] A.Tarca / 2007 / Machine Learning and Its Applications to Biology / PLoS Computational Biology 3 (6) : 953~963

[journal] Y.Zhang / 2007 / Bayesian inference of epistatic interactions in case-control studies / Nature Genetics 39 (9) : 1167~1173

[journal] M. Ritchie / 2001 / Multifactordimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer / American Journal of Human Genetics 69 (1) : 138~147

[journal] C.Kooperberg / 2001 / Sequence analysis using logic regression / Genetic epidemiology 21 : 626~631

[journal] M.Nelson, / 2001 / A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation / Genome Research 11 : 458~470

[journal] R.Culverhouse, / 2004 / Detecting epistatic interactions contributing to quantitative traits / Genetic Epidemiology, 27 (2) : 141~152

[journal] C.Kooperberg / 2005 / Identifying interacting SNPs using Monte Carlo logistic regression / Genetic Epidemiology, 28 (2) : 157~170

[journal] X.Chen / 2007 / A forest-based approach to identifying gene and gene-gene interactions / Proceedings of the National Academy of Sciences of the United States of America, 104 (49) : 19199~19203

[journal] X.Wan, / 2009 / MegaSNPHunter:a learning approach to detect disease prediction SNPs and high level interactions in genome wide association study / BMC Bioinformatics, 10 (13)

[book] T.Cover / 2006 / Elements of information theory / Wiley

[book] 이재원 / 2005 / 생명과학 연구를 위한 통계적 방법 / 자유 아카데미

[journal] S. Kim / 2005 / Polymorphism of tandem repeat in promoter of 5-lipoxygenase in ASA-intolerant asthma: a positive association with airway hyperresponsiveness / Allergy 60 (6) : 760~765

[journal] D. Contopoulos-Ioannidis / 2005 / Meta-analysis of the association of beta2-adrenergic receptor polymorphisms with asthma phenotypes / Journal of Allergy and Clinical Immunology 115 (5) : 963~972

[journal] A.Litonjua / 2006 / The significance of beta2-adrenergic receptor polymorphisms in asthma / Current Opinion in Pulmonary Medicine / 12 (1) : 12~17

[journal] K. Fukunaga / 2001 / Genetic polymorphisms of CC chemokine receptor 3 in Japanese and British asthmatics / European Respiratory Journal 17 : 59~46

[journal] S. Kim / 2006 / Cysteinyl leukotriene receptor 1 promoter polymorphism is associated with aspirin-intolerant asthma in males / Clinical & Experimental Allergy 36 (4) : 433~439

[journal] C. Tasi / 2004 / Renin-angiotensin system gene polymorphisms and atrial fibrillation / Circulation 109 (13) : 1640~1646

[journal] J.Moore, / 2003 / Power ofmultifactor dimensionality reduction fordetecting gene-gene interactions in the presence of genotyping error,missing data,phenocopy,and genetic heterogeneity / Genetic Epidemiology 24 (2) : 150~157

[journal] K.Liang / 2006 / An algorithm for model construction and its napplications to pharmacogenomic studies / Journal of Human Genetics 51 : 751~759

[journal] J.Moore, / 2010 / Bioinformatics challenges for genome-wide association studies / Bioinformatics 26 (4) : 445~455

[journal] X.Wan / 2010 / Predictive rule inference for epistatic interaction detection in genome-wide association studies / Bioinformatics 26 (1) : 30~37

[book] T.Cormen / 2009 / Introduction to algorithms / MIT Press

[journal] 신진섭 / 2008 / Development of Diagnosis System through Human-body Information Measurement / 한국컴퓨터정보학회논문지 / 한국컴퓨터정보학회 13 (1) : 219~226

[journal] 김광백 / 2010 / Self Health Diagnosis System of Oriental Medicine Using Enhanced Fuzzy ART Algorithm / 한국컴퓨터정보학회논문지 / 한국컴퓨터정보학회 15 (2) : 27~34
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