Unraveling gene function in agricultural species using gene co-expression networks

Robert J. Schaefer, Jean Michel Michno, Chad L. Myers

Research output: Contribution to journalReview articlepeer-review

34 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)53-63
Number of pages11
JournalBiochimica et Biophysica Acta - Gene Regulatory Mechanisms
Issue number1
StatePublished - Jan 1 2017

Bibliographical note

Funding Information:
RJS and CLM were partially supported by Grant DBI-0953881 and Grant IOS-1126950 from the National Science Foundation. CLM is partially supported by the CIFAR Genetic Networks Program. RJS is supported by Grant 2016-67012-24841 from the National Institute of Food and Agriculture. JMM is supported by a Biomedical Informatics and Computational Biology (BICB) Graduate Fellowship.

Publisher Copyright:
© 2016 Elsevier B.V.

Copyright 2017 Elsevier B.V., All rights reserved.


  • Agriculture
  • Co-expression
  • Crops
  • Functional genomics
  • Guilt-by-association
  • Network analysis


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