Identification and evaluation of functional modules in gene co-expression networks

Jianhua Ruan, Weixiong Zhang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

14 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationSystems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers
Pages57-76
Number of pages20
StatePublished - Dec 1 2007
Externally publishedYes
EventJoint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics - San Diego, CA, United States
Duration: Dec 1 2006Dec 3 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4532 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceJoint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics
CountryUnited States
CitySan Diego, CA
Period12/1/0612/3/06

Keywords

  • Clustering
  • Co-expression networks
  • Community identification
  • Microarray

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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