Gene Co-expression Network Analysis and Linking Modules to Phenotyping Response in Plants

Qian Du, Malachy T. Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Qi Zhang, Chi Zhang

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Environmental factors, including different stresses, can have an impact on the expression of genes and subsequently the phenotype and development of plants. Since a large number of genes are involved in response to the perturbation of the environment, identifying groups of co-expressed genes is meaningful. The gene co-expression network models can be used for the exploration, interpretation, and identification of genes responding to environmental changes. Once a gene co-expression network is constructed, one can determine gene modules and the association of gene modules to the phenotypic response. To link modules to phenotype, one approach is to find the correlated eigengenes of given modules or to integrate all eigengenes in regularized linear model. This manuscript describes the method from construction of co-expression network, module discovery, association between modules and phenotypic data, and finally to annotation/visualization.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages261-268
Number of pages8
DOIs
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
Volume2539
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Association between co-expression network and phenotyping data
  • Data integration
  • Gene co-expression network
  • Module discovery

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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