Identification of Rice Hormone-Related Gene Modules and Key Genes by Weighted Gene Co-Expression Network Analysis

• Main Authors: Pen-Li Lee, 李本立
• Other Authors: Hungyen Chen
• Format: Others
• Language: zh-TW
• Published: 2019
• Online Access: http://ndltd.ncl.edu.tw/handle/54rah6

碩士 === 國立臺灣大學 === 農藝學研究所 === 107 === Plant hormones are organic substances that control the metabolism of plant cells according to their concentration, and play an important role in physiological regulation of plants. This study aims to understand the effects of different plant hormones on rice gene expression, and identify plant hormone-related clusters of genes and their key genes. In this study, we downloaded the available microarray data sets of rice with six kinds of plant hormone treatments from GEO. 22991 differential expression genes were selected by the analyses of variance (ANOVA), and categorized into gene modules 1 to 16 by weighted gene co-expression network analysis (WGCNA). Heatmaps and biplots were used to visualize the results of the root and shoot samples. In root samples, gene modules 3, 4, 5, 7, 11, and 12 are more related to abscisic acid, jasmonates, abscisic acid or auxin, brassinolides, cytokinin, and gibberellin respectively. In shoot samples, gene modules 1, 2, 3, 6, and 7 are more related to brassinolides, jasmonates, abscisic acid, gibberellin or cytokinin, and abscisic acid or auxin respectively. In each gene module, we set the thresholds of kIM and kME to screen the genes that have high connectivity to the other genes and high correlation to the eigen gene. These genes are called key genes, and some of the key genes have been confirmed that they have relation with specific plant hormones. It is helpful to explain the relationship between different plant hormone treatments and gene modules through the heatmaps and biplots. Finally, the key genes may serve as a reference for future studies about plant hormones and gene function.