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Article
Regulon organization of Arabidopsis
BMC Plant Biology
  • Wieslawa I Mentzen, CRS4 Bioinformatics Laboratory
  • Eve S. Wurtele, Iowa State University
Document Type
Article
Publication Version
Published Version
Publication Date
1-1-2008
DOI
10.1186/1471-2229-8-99
Abstract
Background: Despite the mounting research on Arabidopsis transcriptome and the powerful tools to explore biology of this model plant, the organization of expression of Arabidopsis genome is only partially understood. Here, we create a coexpression network from a 22,746 Affymetrix probes dataset derived from 963 microarray chips that query the transcriptome in response to a wide variety of environmentally, genetically, and developmentally induced perturbations. Results: Markov chain graph clustering of the coexpression network delineates 998 regulons ranging from one to 1623 genes in size. To assess the significance of the clustering results, the statistical over-representation of GO terms is averaged over this set of regulons and compared to the analogous values for 100 randomly-generated sets of clusters. The set of regulons derived from the experimental data scores significantly better than any of the randomly-generated sets. Most regulons correspond to identifiable biological processes and include a combination of genes encoding related developmental, metabolic pathway, and regulatory functions. In addition, nearly 3000 genes of unknown molecular function or process are assigned to a regulon. Only five regulons contain plastomic genes; four of these are exclusively plastomic. In contrast, expression of the mitochondrial genome is highly integrated with that of nuclear genes; each of the seven regulons containing mitochondrial genes also incorporates nuclear genes. The network of regulons reveals a higher-level organization, with dense local neighborhoods articulated for photosynthetic function, genetic information processing, and stress response. Conclusion: This analysis creates a framework for generation of experimentally testable hypotheses, gives insight into the concerted functions of Arabidopsis at the transcript level, and provides a test bed for comparative systems analysis.
Comments

This article is from BMC Plant Biology 8 (2008): 99, doi: 10.1186/1471-2229-8-99. Posted with permission.

Rights
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright Owner
Mentzen and Wurtele
Language
en
File Format
application/pdf
Citation Information
Wieslawa I Mentzen and Eve S. Wurtele. "Regulon organization of Arabidopsis" BMC Plant Biology Vol. 8 (2008) p. 99
Available at: http://works.bepress.com/eve-wurtele/41/