利用加權基因共表現網路鑑別水稻荷爾蒙相關之基因模塊與關鍵基因

Abstract

植物荷爾蒙是能根據其濃度影響植物細胞代謝的有機物，對植物生理調控有相當的重要性。本研究目的在於了解不同植物荷爾蒙對水稻基因表現量的影響，找出易受植物荷爾蒙影響的基因群，並從中選出較為關鍵之基因。研究數據為NCBI資料庫中下載的六種植物荷爾蒙處理之水稻微陣列資料，以變異數分析從中篩選出22991個差異表現基因，並利用加權基因共表現網路(WGCNA)的分析方式將差異表現基因分成基因模塊1至16，再透過熱圖和雙軸圖將根部與莖部的樣本分別進行視覺化。在根的樣本組中，基因模塊3、4、5、7、11、12分別與離層酸、茉莉酸、離層酸或生長素、蕓苔素内酯、細胞分裂素、吉貝素有較高的關聯性；在莖的樣本組中，基因模塊1、2、3、6、7與蕓苔素内酯、茉莉酸、離層酸、吉貝素或細胞分裂素、離層酸或生長素有較高的關聯性。接著利用kIM和kME值挑選在基因模組中與其他基因有較高關聯性且與特徵基因較為相關之基因，稱之為關鍵基因，而其中部分關鍵基因已被證實與特定植物荷爾蒙有所關聯。藉由熱圖和雙軸圖的輔助，有助於解釋不同荷爾蒙處理與基因模塊之間的關係。最終篩選出的關鍵基因則能提供日後植物荷爾蒙和基因功能之相關研究的參考。

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.