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

  • Conference paper
Systems Biology and Computational Proteomics (RSB 2006, RCP 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4532))

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 algorithms, such as k-means, self-organizing maps, and spectral clustering, and have high agreement to the modular structures in the reference networks.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis MO 63130, USA

    Jianhua Ruan & Weixiong Zhang

  2. Department of Genetics, Washington University in St. Louis, St. Louis MO 63130, USA

    Weixiong Zhang

Authors
  1. Jianhua Ruan
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  2. Weixiong Zhang
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Trey Ideker Vineet Bafna

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Ruan, J., Zhang, W. (2007). Identification and Evaluation of Functional Modules in Gene Co-expression Networks. In: Ideker, T., Bafna, V. (eds) Systems Biology and Computational Proteomics. RSB RCP 2006 2006. Lecture Notes in Computer Science(), vol 4532. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73060-6_5

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  • DOI: https://doi.org/10.1007/978-3-540-73060-6_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73059-0

  • Online ISBN: 978-3-540-73060-6

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