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Multinetwork Analysis of Arabidopsis Genome

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(A) Networks in their simplest forms are made up of nodes and the edges that connect them. (B) Various types of node connections can be displayed using colors and shapes that indicate different types of molecules and the relationships between them. (C) Multinetwork representation of Arabidopsis metabolic, regulatory, and predicted regulatory connections between genes, proteins, and metabolites (Gutiérrez et al. 2007; Gifford et al. 2006). Specifically, the data used to draw edges comes from (i) information about metabolic reactions and pathways from the KEGG and AraCyc databases; (ii) known DNA : protein regulatory interactions from the Transfac and AGRIS databases; (iii) predicted protein : protein interactions based on homology to experimentally verified protein : protein interactions in Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans using the Interologapproach (Gutiérrez et al. 2007); (iv) predicted relationships between microRNAs and their targets (provided by Pam Green and Blake Meyers, Delaware Biotechnology Institute, University of Delaware, USA); and (v) known interactions between genes or proteins gleaned from published literature using the text-mining tool GeneWays (A. Rhetzsky, University of Chicago). The Cytoscape software is used to visualize the multinetwork in an interactive way (Shannon et al. 2003); (vi) the multinetwork can then be queried to find regulatory subnetworks and interactions between a subset of genes. [Source: Gifford, M. L., R. A. Gutiérrez, and G. M. Coruzzi. 2006. "Modeling the Virtual Plant: A Systems Approach to Nitrogen-Regulatory Gene Networks,"Essay 12.2, Chapter 12: Assimilation of mineral nutrients (https://4e.plantphys.net/ article.php?ch=12&id=352). In A Companion to Plant Physiology, Fourth Edition by L. Taiz and E. Zeiger. Sinauer Associates, Inc., Publishers, Sunderland, Mass. (see also www.virtualplant.org and Gutiérrez et al. 2007).]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 100) (website)

Biological and Environmental Research Information System, Oak Ridge National Laboratory, Oak Ridge, TN genomicscience.energy.gov/ and genomics.energy.gov/