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2006
Springer

Identification and Evaluation of Functional Modules in Gene Co-expression Networks

10 years 11 months ago
Identification and Evaluation of Functional Modules in Gene Co-expression Networks
Abstract. Identifying gene functional modules is an important step towards elucidating gene functions at a global scale. In this paper, we introduce a simple method to construct gene co-expression networks from microarray data, and then propose an efficient spectral clustering algorithm to identify natural communities, which are relatively densely connected sub-graphs, in the network. To assess the effectiveness of our approach and its advantage over existing methods, we develop a novel method to measure the agreement between the gene communities and the modular structures in other reference networks, including protein-protein interaction networks, transcriptional regulatory networks, and gene networks derived from gene annotations. We evaluate the proposed methods on two large-scale gene expression data in budding yeast and Arabidopsis thaliana. The results show that the clusters identified by our method are functionally more coherent than the clusters from several standard clustering...
Jianhua Ruan, Weixiong Zhang
Added 03 Dec 2009
Updated 03 Dec 2009
Type Conference
Year 2006
Where RECOMB
Authors Jianhua Ruan, Weixiong Zhang
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