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Phenotype prediction by integrative network analysis of SNP and gene expression microarrays.


ABSTRACT: A long-term goal of biomedical research is to decipher how genetic processes influence disease formation. Ubiquitous and advancing microarray technology can measure millions of DNA structural variants (single-nucleotide polymorphisms, or SNPs) and thousands of gene transcripts (RNA expression microarrays) in cells. Both of these information modalities can be brought to bear on disease etiology. This paper develops a Bayesian network-based approach to integrate SNP and expression microarray data. The network models SNP-gene interactions using a phenotype-centric network. Inferring the network consists of two steps: variable selection and network learning. The learned network illustrates how functionally dependent SNPs and genes influence each other, and also serves as a predictor of the phenotype. The application of the proposed method to a pediatric acute lymphoblastic leukemia dataset demonstrates the feasibility of our approach and its impact on biological investigation and clinical practice.

SUBMITTER: Chang HH 

PROVIDER: S-EPMC3343740 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Phenotype prediction by integrative network analysis of SNP and gene expression microarrays.

Chang Hsun-Hsien HH   McGeachie Michael M  

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 20110101


A long-term goal of biomedical research is to decipher how genetic processes influence disease formation. Ubiquitous and advancing microarray technology can measure millions of DNA structural variants (single-nucleotide polymorphisms, or SNPs) and thousands of gene transcripts (RNA expression microarrays) in cells. Both of these information modalities can be brought to bear on disease etiology. This paper develops a Bayesian network-based approach to integrate SNP and expression microarray data.  ...[more]

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