臺灣博碩士論文加值系統

抵禦農業中的天氣不穩定性是農業的主要任務之一，為了最大程度地減少收成損失，了解計劃生長，新陳代謝和抵抗環境的機制非常重要。在環境壓力下，在不同濃度植物激素下植物細胞的代謝和生理調節中起著至關重要的作用。
為了全面了解基因的功能（特異性）和基因之間的關係（協同作用），在不同植物激素下進行基因網絡研究非常重要。在這項研究中，從網絡開源數據庫下載的不同植物激素下的微陣列基因表達數據，並構建了加權基因共表達網絡。此外，為了研究基因模塊和植物激素之間的非線性關係，在使用奇異值分解和雙標圖之前，使用子組本質相關係數（subCID）來代替了先前研究所使用取特徵基因模塊表現量的平均。為了清楚的觀察基因模塊在不同植物激素下在不同組織部位中表達水平的變化,計算在雙標圖中基因模塊和不同植物激素處理之間的角度，並進行統計檢驗。
研究結果發現，大多數基因模塊對根和芽組織中植物激素的反應均不同，而相同基因模塊對根和芽組織中植物激素的反應也不同，也在基因本體分析和文獻研究中得到證實。此外，利用subCID還發現了不同植物激素下基因模塊之間的基因協同作用。因此，依據本研究的分析結果，可提供跟先前研究不同的統計方法，用於研究微陣列數據中更準確的基因協同作用和特異性。

Resisting the atmospheric instability in agriculture is one of the major missions in agriculture. In order to minimize the loss of harvest, understanding the mechanism of plan growth, metabolism and resistance to environmental stress is of great importance. During environmental stresses, plant hormones play a critical role in the metabolism and physiological regulation of plant cells in different concentrations.
In order to understand comprehensively the functions of genes (specificity) and relationships between genes (synergy), genes network studies under different plant hormones is of great importance. In this study, the microarray expression data under plant hormones was downloaded from public available database and to construct the weighted gene co-expression network. Furthermore, in order to study the non-linear relationships between genes modules and plant hormones, the subgroup of coefficient of intrinsic dependence (subCID) was also used instead of taking average expression levels of eigengenes modules before singular value decomposition and biplot. The biplot was plotted for clearly visualizing the gene modules changing their expression levels under different conditions in different tissue parts. The angles between genes modules and treatments in biplot were calculated and tested with statistical significance.
Results show that most genes modules response specifically to hormone treatments and same gene modules response differently to plant hormones in root and shoot tissues and the fact that suggests their different roles in different tissues are validated in gene ontology analysis and literature research. In addition, the synergies of genes among genes modules under plant hormones were also found by subCID.

口試委員會審定書………………………………………….………….………....…#
誌謝………………………………………………….………….……..…………………i
摘要………………………………………………………………..…………………….ii
Abstract...…………………………………………………………………………..…...iii
Table of Contents…………...………………………………………………………......iv
List of Figures……….…………………………….……................................................vi
List of Tables……….…………………………….……................................................vii
Chapter1 Introduction…………………………………………………….……………...1
1.1 Plant hormones and Oryza sativa……………………………..…………………..1
1.2 Relation between plant hormones and gene expressions……..…………......…….3
1.3 Microarray gene expression platform…….……………………….………..……..3
1.4 Applications of microarrays…..………………………..……………………...….4
1.5 Weighed gene co-expression network analysis and gene modules……………….5
1.6 Specificity and synergy of gene modules………………………………..……......5
1.7 Objective of this study………………………..…………………………………...6
Chapter 2 Methods of Analysis…………………………………………….....................7
2.1 Data processing before analysis……......................................................................7
2.2 Differential expression genes selection...................................................................7
2.3 WGCNA and subCID……………………………………………...……………...8
2.3.1 Weighted correlation network analysis (WGCNA)…………………..…....…....9
2.3.2 subCID (subgroup of coefficient of intrinsic dependence (CID))……………..11
2.3.3 Inner product of biplot…………………………………………………………12
2.4 Gene Ontology Analysis…………………………..……………………………..13
Chapter 3 Results……………..………………………………………..…….................15
3.1 Data processing and differential expression genes selection…….........................15
3.2 Identification of gene modules by WGCNA and subCID.....................................15
3.3.1 Non-subCID part: comparison of p-values of inner products between each gene modules and each plant hormone treatment between root and shoot……….……….16
3.3.2 subCID part: comparison of p-values of inner products between each gene modules and each plant hormone treatment between root and shoot……………......17
3.3.3 Comparison between gene modules response to plant hormones in different tissues in WGCNA versus subCID………………………………………………......18
3.4 Gene Ontology study on gene modules…………………………………….........19
3.4.1 Comparison between subCID and nonsubCID in root and shoot tissue in terms of gene ontology……………………………………………………………..………20
Chapter 4 Discussion…………………………………...................................................21
Chapter 5 Conclusion…………………………………………………………..............27
Reference…………….…………………………………………....................................29
Supplementary files……….…………………………….…….......................................43

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