Unraveling gene function in agricultural species using gene co-expression networks |
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Authors: | Robert J Schaefer Jean-Michel Michno Chad L Myers |
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Institution: | 1. Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States;2. Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, United States |
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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. |
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Keywords: | Co-expression Functional genomics Agriculture Crops Network analysis Guilt-by-association |
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