title: Unraveling gene function in agricultural species using gene co-expression networks.
abstract: Co-expression networks have been shown to be a powerful tool for inferring a gene's function when little is known about it. With the advent of next generation sequencing technologies, the construction and analysis of co-expression networks is now possible in non-model species, including those with agricultural importance. Here, we review fundamental concepts in the construction and application of co-expression networks with a focus on agricultural crops. We survey past and current applications of co-expression network analysis in several agricultural species and provide perspective on important considerations that arise when analyzing network relationships. We conclude with a perspective on future directions and potential challenges of utilizing this powerful approach in crops. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
authors.affiliation: Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schaefer
authors.affiliation: Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Michno
authors.affiliation: Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, United States. Electronic address: cmyers@cs.umn.edu.
authors.forename: Chad L
authors.initials: CL
authors.lastname: Myers
mesh_terms: D000383:Agriculture / Q000379:methods; D018556:Crops, Agricultural / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*
keywords: Agriculture; Co-expression; Crops; Functional genomics; Guilt-by-association; Network analysis