SNP and gene networks construction and analysis from classification of copy number variations data

BMC Bioinformatics

Proceedings

Yiu Fai Lee¹  Michael K Ng¹  Yang Liu¹ 

[1] Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong;

关键词: Single Nucleotide Polymorphism;    Copy Number Variation;    Single Nucleotide Polymorphism Array;    Wellcome Trust Case Control Consortium;    Single Nucleotide Polymorphism Position;   

DOI  :  10.1186/1471-2105-12-S5-S4

来源: Springer

【 摘 要 】

BackgroundDetection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. It is interesting to identify and represent relevant CNVs from a genome-wide data due to high data volume and the complexity of interactions.ResultsIn this paper, we incorporate the DNA copy number variation data derived from SNP arrays into a computational shrunken model and formalize the detection of copy number variations as a case-control classification problem. More than 80% accuracy can be obtained using our classification model and by shrinkage, the number of relevant CNVs to disease can be determined. In order to understand relevant CNVs, we study their corresponding SNPs in the genome and a statistical software PLINK is employed to compute the pair-wise SNP-SNP interactions, and identify SNP networks based on their P-values. Our selected SNP networks are statistically significant compared with random SNP networks and play a role in the biological process. For the unique genes that those SNPs are located in, a gene-gene similarity value is computed using GOSemSim and gene pairs that have similarity values being greater than a threshold are selected to construct gene networks. A gene enrichment analysis show that our gene networks are functionally important.Experimental results demonstrate that our selected SNP and gene networks based on the selected CNVs contain some functional relationships directly or indirectly to disease study.ConclusionsTwo datasets are given to demonstrate the effectiveness of the introduced method. Some statistical and biological analysis show that this shrunken classification model is effective in identifying CNVs from genome-wide data and our proposed framework has a potential to become a useful analysis tool for SNP data sets.

【 授权许可】

Unknown   
© Liu et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.