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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 劉力瑜(Li-Yu Liu) | |
| dc.contributor.author | Po-Chih Shen | en |
| dc.contributor.author | 沈柏志 | zh_TW |
| dc.date.accessioned | 2021-06-17T01:47:18Z | - |
| dc.date.available | 2020-08-25 | |
| dc.date.copyright | 2017-08-25 | |
| dc.date.issued | 2017 | |
| dc.date.submitted | 2017-07-26 | |
| dc.identifier.citation | Albert R (2005) Scale-free networks in cell biology. J Cell Sci 118:4947.
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/67743 | - |
| dc.description.abstract | 在建立模型或決策時，找出關鍵特徵變數是很重要的一環。本質相關係數 (coefficient of intrinsic dependence, CID) 是一個關聯統計量，可以用來度量變數間的關聯性。它在一些找尋相關性的應用上有很好的表現，例如用來建立基因調控網路或是測量兩組變數的關聯性。為了更方便給其他人使用，例如生物學家，在本研究中，開發一個R套件(cidr)，讓大家可以更容易且方便的進行本質相關係數計算。本研究也整合加權基因共表現網絡分析 (weighted gene co-expression network analysis, WGCNA) 與本質相關係數 (CID)，應用在找尋阿拉伯芥非生物逆境專一 (abiotic stress-specific) 之基因群，並利用熱圖 (heatmap) 與雙軸圖 (biplot) 來進行視覺化呈現。在低溫、高溫、鹽害逆境下，分別找到2個低溫、3個高溫、5個鹽害逆境專一基因群，提供了解生物交互影響過程的初步參考。此外，我們應用了子本質相關係數 (subCID) 更詳細的在基因群中找尋逆境專一基因，透過各基因 subCID 數值矩陣製作雙軸圖，有助於區分出各個逆境專一的基因。希望本論文開發之 cidr套件以及論文中描述的方法，有助於揭示隱藏在大規模基因體數據中的相關生物機制。 | zh_TW |
| dc.description.abstract | Feature selection plays an important rule for modeling or decision making. The coefficient of intrinsic dependence (CID) is an association measure which can be used to measure the relationship among the variables. It had been applied to construct gene regulatory networks and to measure the relationships between two groups of one- or multiple-dimensional variables. For the convenience of potential users to obtain the CID values, we had developed an R package, cidr, for the computation and the visualization of CID. In Chapter 3, we also incorporated the weighted gene co-expression network analysis (WGCNA) and CID to find the abiotic stress-specific gene module in Arabidopsis and the results had be summarized using the heatmaps and biplots. Two cold stress-specific, three heat stress-specific, and five salt stress-specific gene modules were identified, respectively. The results may provide hints about the underlying biological processes. In Chapter 4, we further adopted the subCID values to identify the stress-specific genes in a gene module. The biplot derived from the subCID matrix assisted to visualize the stress-specific genes. In conclusion, we hope the cidr package as well as the methodologies described in the dissertation can assist to reveal the biological insights hidden in massive genomic-level datasets. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-17T01:47:18Z (GMT). No. of bitstreams: 1 ntu-106-D98621202-1.pdf: 3646342 bytes, checksum: 8e1f2d55bec1df9556263ada1a736385 (MD5) Previous issue date: 2017 | en |
| dc.description.tableofcontents | 口試委員審定書 i
誌謝 ii 中文摘要 iii ABSTRACT v LIST OF FIGURES x LIST OF TABLES xi CHAPTER 1 INTRODUCTION 1 CHAPTER 2 cidr: AN R PACKAGE OF CID 4 2.1 Introduction 4 2.2 Materials and Methods 6 2.2.1 The coefficient of intrinsic dependence (CID) 6 2.2.2 Microarray expression data for Demonstration 8 2.2.3 To construct and visualize the GRN via the cidr 9 2.3 Results 13 2.3.1 Constructing gene co-expression networks 13 2.3.2 Gene set association analysis (GSAA) 18 2.4 Discussion 21 2.4.1 Estimated methods under the 1x1y condition 21 2.4.2 Assumption of cidnet’s inputs 22 2.4.3 The occasions for different plot functions 23 2.4.4 Future works 24 2.5 Conclusion 24 CHAPTER 3 ABIOTIC STRESS-SPECIFIC GENE MODULES FOR ARABIDOPSIS 26 3.1 Introduction 26 3.2 Materials and Methods 32 3.3 Results 37 3.4 Discussion 41 3.5 Conclusion 49 CHAPTER 4 APPLICATION OF SUBCID FOR CHOOSING STRESS-SPECIFIC GENES 51 4.1 Introduction 51 4.2 Materials and Methods 52 4.3 Results 55 4.4 Discussion 63 4.5 Conclusion 65 CHAPTER 5 CONCLUSION 66 REFERENCE 69 APPENDIX 76 Supplementary Figures 76 Supplementary Tables 77 List of abbreviations used 80 | |
| dc.language.iso | en | |
| dc.subject | 非生物逆境專一基因群 | zh_TW |
| dc.subject | 本質相關係數 | zh_TW |
| dc.subject | 非生物逆境 | zh_TW |
| dc.subject | 加權基因共表現網絡分析 | zh_TW |
| dc.subject | 雙軸圖 | zh_TW |
| dc.subject | the coefficient of intrinsic dependence | en |
| dc.subject | abiotic stress-specific gene module | en |
| dc.subject | biplot | en |
| dc.subject | the weighted gene co-expression network analysis | en |
| dc.subject | abiotic stress | en |
| dc.title | 本質相關係數套件cidr 及其應用 - 以找尋阿拉伯芥非生物逆境專一之基因群為例 | zh_TW |
| dc.title | cidr: A Package of Coefficient of Intrinsic Dependence (CID) and its Application of Finding the Abiotic Stress-specific Gene Modules in Arabidopsis | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 105-2 | |
| dc.description.degree | 博士 | |
| dc.contributor.oralexamcommittee | 侯譪玲(Ai-Ling Hour),謝邦昌(Ben-Chang Shia),廖振鐸(Chen-Tuo Liao),蔡政安(Chen-An Tsai) | |
| dc.subject.keyword | 本質相關係數,非生物逆境,加權基因共表現網絡分析,雙軸圖,非生物逆境專一基因群, | zh_TW |
| dc.subject.keyword | the coefficient of intrinsic dependence,abiotic stress,the weighted gene co-expression network analysis,biplot,abiotic stress-specific gene module, | en |
| dc.relation.page | 81 | |
| dc.identifier.doi | 10.6342/NTU201701822 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2017-07-26 | |
| dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
| dc.contributor.author-dept | 農藝學研究所 | zh_TW |
| 顯示於系所單位： | 農藝學系 | |
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