TY - CHAP
T1 - Gene Co-expression Network Analysis and Linking Modules to Phenotyping Response in Plants
AU - Du, Qian
AU - Campbell, Malachy T.
AU - Yu, Huihui
AU - Liu, Kan
AU - Walia, Harkamal
AU - Zhang, Qi
AU - Zhang, Chi
N1 - Publisher Copyright:
© 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - Association between co-expression network and phenotyping data
KW - Data integration
KW - Gene co-expression network
KW - Module discovery
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U2 - 10.1007/978-1-0716-2537-8_20
DO - 10.1007/978-1-0716-2537-8_20
M3 - Chapter
C2 - 35895209
AN - SCOPUS:85135376529
T3 - Methods in Molecular Biology
SP - 261
EP - 268
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -