Gene Regulation Network Inference With Joint Sparse Gaussian Graphical Models

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Revealing biological networks is one key objective in systems biology. With microarrays, researchers now routinely measure expression profiles at the genome level under various conditions, and such data may be used to statistically infer gene regulation networks. Gaussian graphical models (GGMs) have proven useful for this purpose by modeling the Markovian dependence among genes. However, a single GGM may not be adequate to describe the potentially differing networks across various conditions, and hence it is more natural to infer multiple GGMs from such data. In this article we propose a class of nonconvex penalty functions aiming at the estimation of multiple GGMs with a flexible joint sparsity constraint. We illustrate the property of our proposed nonconvex penalty functions by simulation study. We then apply the method to a gene expression dataset from the GenCord Project, and show that our method can identify prominent pathways across different conditions. Supplementary materials for this article are available online.
Publisher
AMER STATISTICAL ASSOC
Issue Date
2015-10
Language
English
Article Type
Article
Citation

JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS, v.24, no.4, pp.954 - 974

ISSN
1061-8600
DOI
10.1080/10618600.2014.956876
URI
http://hdl.handle.net/10203/264307
Appears in Collection
MA-Journal Papers(저널논문)
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