Cluster Analysis of SNPs with Entropy Distance and Prediction of Asthma Type Using SVM


KIPS Transactions on Computer and Communication Systems, Vol. 18, No. 2, pp. 67-72, Apr. 2011
10.3745/KIPSTB.2011.18.2.67,   PDF Download:

Abstract

Single nucleotide polymorphisms (SNPs) are a very important tool for the study of human genome structure. Cluster analysis of the large amount of gene expression data is useful for identifying biologically relevant groups of genes and for generating networks of gene-gene interactions. In this paper we compared the clusters of SNPs within asthma group and normal control group obtained by using hierarchical cluster analysis method with entropy distance. It appears that the 5-cluster collections of the two groups are significantly different. We searched the best set of SNPs that are useful for diagnosing the two types of asthma using representative SNPs of the clusters of the asthma group. Here support vector machines are used to evaluate the prediction accuracy of the selected combinations. The best combination model turns out to be the five-locus SNPs including one on the gene ALOX12 and their accuracy in predicting aspirin tolerant asthma disease risk among asthmatic patients is 66.41%.


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Cite this article
[IEEE Style]
J. S. Lee, K. S. Shin and K. B. Wee, "Cluster Analysis of SNPs with Entropy Distance and Prediction of Asthma Type Using SVM," KIPS Journal B (2001 ~ 2012) , vol. 18, no. 2, pp. 67-72, 2011. DOI: 10.3745/KIPSTB.2011.18.2.67.

[ACM Style]
Jun Seob Lee, Ki Seob Shin, and Kyu Bum Wee. 2011. Cluster Analysis of SNPs with Entropy Distance and Prediction of Asthma Type Using SVM. KIPS Journal B (2001 ~ 2012) , 18, 2, (2011), 67-72. DOI: 10.3745/KIPSTB.2011.18.2.67.