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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/48009完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 曾宇鳳(Y. Jane Tseng) | |
| dc.contributor.author | Tze-Feng Tian | en |
| dc.contributor.author | 田士鋒 | zh_TW |
| dc.date.accessioned | 2021-06-15T06:44:22Z | - |
| dc.date.available | 2016-08-23 | |
| dc.date.copyright | 2011-08-23 | |
| dc.date.issued | 2011 | |
| dc.date.submitted | 2011-08-19 | |
| dc.identifier.citation | [1] L. Mondello, et al., 'Comprehensive two-dimensional gas chromatography-mass spectrometry: a review,' Mass Spectrom Rev, vol. 27, pp. 101-24, Mar-Apr 2008.
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/48009 | - |
| dc.description.abstract | 這篇論文包含了三個主題，第一個主題是二維氣相層析質譜圖的滯留時間校準演算法，第二個主題是3Omics：整合轉錄體學,蛋白質體學與代謝體學之系統生物學網路視覺化工具，第三個主題是人類代謝本體資料庫。
二維氣相層析質譜圖 (GCxGC-MS) 在代謝體實驗分析上帶來了更佳的分離能力，選擇性與靈敏度。在分析過程中，隨著時間或無法控制的環境因素如溫度，壓力，基質效應，或靜相降解將會造成分批注入的同樣樣品或不同樣品上的同個訊號在層析圖滯留時間上有所偏移。本篇開發的滯留時間校正演算法－2DGCMS-aligner，能夠直接使用由儀器產生的netCDF格式，偵測層析質譜圖上的訊號並使用歐式距離與Pearson相關係數來校正偏移的訊號。這個演算法已被實作成一套完整的GCxGC-MS數據分析軟體。這個軟體的功能包含了基線校正，波峰偵測，滯留時間校正與數據視覺化，可用在常規的分析上。此滯留時間演算法使用了在不同實驗條件下產生的數據作為展示並有效的矯正了滯留時間的偏移，在計算的準確度上勝於現有的滯留時間校正演算法。 3Omics 是一個能夠整合系統生物學的網路視覺化工具。它能快速整合人體的轉錄體，蛋白質體與代謝體的實驗數據以分析其關聯性並將結果視覺化。一個生化反應的上中下游之分析經整合轉錄體，蛋白質體與代謝體數據，可在3Omics透過相關網路分析 (Correlation Network)，共同表現分析 (Co-expression)，表現型分析 (Phenotyping)，KEGG生物途徑集分析 (KEGG Pathway Enrichment) 與基因本體集 (GO enrichment) 分析而理解人體系統如何行使功能。3Omics透過相關網路來顯示在時間序列或不同實驗條件上的生物組學之間的關係。若三種生物組學的數據中缺少一種，3Omics會使用PubMed文獻資料庫中的轉錄體，蛋白質體與代謝體資訊來填補。共同表現分析能夠協助探索生物組學間的共同功能。表現型分析整合了人類孟德爾遺傳學資料庫的資料。KEGG生物途徑富集分析使用代謝體的數據並在KEGG資料庫中探索富集的生物途徑。基因本體富集分析幫助使用者找出顯著表現的轉錄數據所對應的基因本體。3Omics將現有的軟體之優點與功能納入其中，簡化了數據分析的程序並讓使用者只需要簡單的操作就能夠得到分析的結果。視覺化與分析結果也可讓使用者下載作為後續的分析使用。使用者可以到http://cmdd.csie.ntu.edu.tw/~3omics免費取得並使用。 在最後的章節中，我們建立了人類代謝本體資料庫 (Human Metabolome Ontology)。目前在代謝體的分析流程中，對於代謝體的生物意義進行評估與解釋需要手動收集各種零散的文獻如Gene Ontology，BRENDA，KEGG Brite，KEGG Pathway，人類代謝體資料庫，OMIM等等工程繁瑣。我們開發了人類代謝本體資料庫 (HMO) 來加速整合各種代謝體功能，代謝體化學結構分類以及代謝體與其交互作用的目標，藉此能夠為後續的計算分析提供穩健的基礎生醫知識架構。HMO提供了三個獨立的本體：生物功能，化學結構分類與代謝體目標。生物功能是指代謝體所涉及的代謝途徑。化學性質分類闡述了代謝體的來源如內生性或衍生性，以及其化學結構分類如碳水化合物，脂質。代謝體目標提供了代謝體作用的目標物，其代謝體組成與其他代謝體之交互作用，以及目標在組織或細胞的所在位置。HMO以Open Biomedical Ontology (OBO) 的格式架設在擁有友善介面的網路應用程式上。目前的HMO版本包含了16120個代謝物，1840個代謝體目標以及161個與代謝體相關的疾病。HMO的名詞包含了408個生物功能，129個化學性質分類，以及22837個代謝體目標。HMO在本體領域上建立了詳盡的代謝體資源資料庫中心，讓使用者能夠利用與共享資源。使用者可以到http://cmdd.csie.ntu.edu.tw/~hmo免費取得並使用。 | zh_TW |
| dc.description.abstract | Three works are included in this thesis including 1) an algorithm for Comprehensive two-dimensional gas chromatography mass spectrometry alignment, 2) 3Omics: a web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data, and 3) HMO: a tool for understanding the human metabolome.
A novel peak alignment algorithm, 2DGCMS-aligner, has been developed for two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS) data. 2DGCMS-aligner uses the netCDF data generated from the instrument as input directly. It detects blobs, clusters of pixels that are brighter or darker than their surround in a chromatogram, of each GCxGC/TOF-MS raw data to generate blob tables instead of peak tables to perform alignment. 2DGCMS-aligner correlates the blobs with Euclidean distance of the first- and second retention times in the blob tables and the mass spectra with Pearson’s correlation coefficient. This alignment algorithm in 2DGCMS-aligner can be applied to GCxGC-MS data generated by either consistent or inconsistent instrument environment to adjust retention time shifts along both chromatographic dimensions caused by uncontrollable fluctuations in temperature and pressure, matrix effects and stationary phase degradation. 2DGCMS-aligner also includes an option to correct baseline on raw data directly. The performance of 2DGCMS-aligner peak alignment algorithm was compared and demonstrated with three existing alignment methods on the two sets of GCxGC-MS data sets acquired in different experiment conditions and a mixture of standard metabolites. 3Omics: a web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data was developed to visualize and rapidly integrate multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. A biochemical cascade is generated through consolidation of transcript, protein, and metabolite data and implements via the application of five commonly used analyses of correlation network, co-expression, phenotyping, KEGG pathway enrichment, and GO enrichment. 3Omics incorporates the advantages and operations of existing software into a single platform, therefore simplifying the data analysis procedure and enabling the user to perform a one-click integrated analysis for free. Visualization and analysis results are downloadable for further user customization and analysis. The 3Omics software can be freely accessed at http://cmdd.csie.ntu.edu.tw/~3omics. Last part of this thesis work is the construction of Human Metabolome Ontology (HMO). Final step in current metabolomics studies involves assessment and biological interpretation of metabolome. It often requires tedious manual collections of literature or linking information scattered in Gene Ontology, BRENDA, KEGG Brite, KEGG Pathway, Human Metabolome Database, OMIM and so on. We developed the HMO to facilitate integration of biological functions, and chemical classification of metabolome and comprehensive understanding of metabolome and its target interactions as the common language and knowledge framework allowing further computational analysis. HMO consists of three independent ontologies: biological functions, chemical taxonomies and metabolome targets. It provides a comprehensive metabolome centered resource that enables the sharing and reuse of the know-ledge across domains of ontologies. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-15T06:44:22Z (GMT). No. of bitstreams: 1 ntu-100-R98922152-1.pdf: 5615436 bytes, checksum: e792d0142c0d87d3851f9ec67cbac195 (MD5) Previous issue date: 2011 | en |
| dc.description.tableofcontents | 口試委員會審定書 i
誌謝 ii 中文摘要 iii ABSTRACT v CONTENTS vii LIST OF FIGURES x LIST OF TABLES xiv Chapter 1 An Algorithm for Comprehensive Two-dimensional Gas Chromatography Mass Spectrometry Alignment 1 1.1 Introduction 1 1.2 Materials 6 1.2.1 Mixture of Standard Compounds of Angelica sinensis 6 1.2.2 GCxGC-MS Analysis 6 1.3 2DGCMS-aligner Algorithm 7 1.3.1 Data Preprocessing 7 1.3.2 Baseline Correction 8 1.3.3 Blob Detection 10 1.3.4 Alignment 11 1.3.5 Comparison of 2DGCMS-aligner alignment algorithm with mSORT, DISCO and mSPA 13 1.4 Results and Discussion 16 1.4.1 Baseline Correction 17 1.4.2 Blob Detection 21 1.4.3 Alignment 23 1.4.4 Evaluation for 2DGCMS-aligner alignment algorithm 28 1.5 Conclusion 31 Chapter 2 3Omics: a web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data 32 2.1 Introduction 32 2.2 Design and Implementation 36 2.2.1 System Overview 36 2.2.2 Correlation analysis 36 2.2.3 Co-expression analysis 38 2.2.4 Phenotype Analysis 39 2.2.5 KEGG pathway enrichment analysis 39 2.2.6 Gene Ontology-based functional enrichment analysis 40 2.3 Results 40 2.3.1 Summary of 3Omics’ features 40 2.3.2 Main functions of 3Omics and case study 43 2.3.3 Comparison of 3Omics and other software 49 2.3.4 Case studies 51 Chapter 3 HMO: a tool for understanding the human metabolome 59 3.1 Introduction 59 3.2 HMO Ontologies 62 3.2.1 Three Ontologies of HMO 62 3.2.2 Ontology hierarchy 63 3.3 Implementation 67 3.3.1 Architecture 67 3.3.2 Term Information 68 3.3.3 Searching 69 3.3.4 Browsing 71 3.4 Discussion 73 3.5 Conclusion 76 REFERENCE 77 APPENDIX 84 | |
| dc.language.iso | en | |
| dc.subject | 代謝體學 | zh_TW |
| dc.subject | 二維氣相層析質譜圖滯留時間校正 | zh_TW |
| dc.subject | 2DGCMS-aligner | zh_TW |
| dc.subject | 系統生物學的網路視覺化工具 | zh_TW |
| dc.subject | 人類代謝本體資料庫 | zh_TW |
| dc.subject | 2DGCMS-aligner | en |
| dc.subject | Metabolomics | en |
| dc.subject | Human Metabolome Ontology | en |
| dc.subject | Systems Biology Visualization | en |
| dc.subject | 2DGC alignment | en |
| dc.title | 二維氣相層析質譜圖之滯留時間校準演算法 | zh_TW |
| dc.title | Alignment Algorithm for Comprehensive Two-dimensional Gas Chromatography-Mass Spectrometry | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 99-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 陳家揚(Chia-Yang Chen),李宏萍(Hong-Ping Li),郭錦樺(Ching-Hua Kuo) | |
| dc.subject.keyword | 二維氣相層析質譜圖滯留時間校正,2DGCMS-aligner,系統生物學的網路視覺化工具,人類代謝本體資料庫,代謝體學, | zh_TW |
| dc.subject.keyword | 2DGC alignment,2DGCMS-aligner,Systems Biology Visualization,Human Metabolome Ontology,Metabolomics, | en |
| dc.relation.page | 91 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2011-08-20 | |
| dc.contributor.author-college | 電機資訊學院 | zh_TW |
| dc.contributor.author-dept | 電機工程學研究所 | zh_TW |
| 顯示於系所單位： | 電機工程學系 | |
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