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Gene Co-expression Network Analysis

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Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2443))

Abstract

Gene co-expression analysis is a data analysis technique that helps identify groups of genes with similar expression patterns across several different conditions. By means of these techniques, different groups have been able to assign putative metabolic pathways and functions to understudied genes and to identify novel metabolic regulation networks for different metabolites. Some groups have even used network comparative studies to understand the evolution of these networks from green algae to land plants. In this chapter, we will go over the basic definitions required to understand network topology and gene module identification. Additionally, we offer the reader a walk-through a standard analysis pipeline as implemented in the package WGCNA that takes as input raw fastq files and obtains co-expressed gene clusters and representative gene expression patterns from each module for downstream applications.

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Author information

Authors and Affiliations

  1. Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria

    Juan D. Montenegro

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  1. Juan D. Montenegro
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Correspondence to Juan D. Montenegro .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Western Australia, Perth, WA, Australia

    David Edwards

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Montenegro, J.D. (2022). Gene Co-expression Network Analysis. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_19

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  • DOI: https://doi.org/10.1007/978-1-0716-2067-0_19

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2066-3

  • Online ISBN: 978-1-0716-2067-0

  • eBook Packages: Springer Protocols

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