NDLI: Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs

Content Provider	IEEE Xplore Digital Library
Author	Rui Jiang Jiaxin Wu
Copyright Year	2011
Description	Author affiliation: MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, 100084, China (Rui Jiang; Jiaxin Wu)
Abstract	Although several successful stories have been produced by genome-wide association (GWA) studies that are based on the common disease-common variant (CD-CV) hypothesis, recent studies have suggested a more general common disease-rare variant (CD-RV) hypothesis in the mapping of disease-associated genetic variants. Consequently, a number of statistical approaches have been proposed to detect associations between rare variants and inherited human diseases. Nevertheless, most of these methods require the selection of functional variants before applying statistical analysis, for the purpose of maximizing the power of statistical tests. To meet this requirement, we propose in this paper a filtration approach to detect genetic variants that are associated with a query disease of interest from the perspective of one-class novelty learning. Focusing on a typical type of genetic variants called nonsynonymous single nucleotide polymorphisms (nsSNPs), we propose to prioritize candidate nsSNPs relying on the integrated use of two sequence conservation features and a domain-domain interaction network. We resort to large-scale leave-one-out cross-validation experiments to assess the effectiveness of the proposed approach and show the power of this approach in detecting nsSNPs that are truly associated with the specific type of disease of interest.
Starting Page	262
Ending Page	267
File Size	757352
Page Count	6
File Format	PDF
ISBN	9781457716126
e-ISBN	9781457716133
DOI	10.1109/BIBMW.2011.6112385
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-11-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins nonsynonymous single nucleotide polymorphisms (nsSNPs) Databases Humans guilt-by-association Genetics Amino acids Bioinformatics data integration Diseases prioritization
Content Type	Text
Resource Type	Article

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