School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA.
Department of Agronomy and Horticulture, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA.
Methods Mol Biol. 2022;2539:261-268. doi: 10.1007/978-1-0716-2537-8_20.
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.
环境因素，包括不同的压力，会对基因的表达产生影响，进而影响植物的表型和发育。由于大量的基因参与了对环境扰动的响应，因此识别共同表达的基因群是有意义的。基因共表达网络模型可用于探索、解释和识别对环境变化有响应的基因。一旦构建了基因共表达网络，就可以确定基因模块以及基因模块与表型响应的关联。为了将模块与表型联系起来，可以找到给定模块的相关特征基因，或者将所有特征基因整合到正则化线性模型中。本文档描述了从共表达网络构建、模块发现、模块与表型数据的关联，最后到注释/可视化的方法。
