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研究生:施宗牧
研究生(外文):Tsung-Mu Shih
論文名稱:SAGE基因表現資料探勘平台之建置
論文名稱(外文):Implementation of Exploration Software for SAGE Data
指導教授:楊正宏楊正宏引用關係
指導教授(外文):Cheng-Hong Yang
學位類別:碩士
校院名稱:國立高雄應用科技大學
系所名稱:電子工程系
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:56
中文關鍵詞:智慧人種基因表現連續分析法SAGE樣本SAGE標籤GEO
外文關鍵詞:Homo sapiensSerial Analysis of Gene Expression (SAGE)SAGE librarySAGE tagGene Expression Omnibus (GEO)
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基因表現連續分析法是一種強而有力的基因表現量化技術,生物之組織或細胞樣本可經由該技術來產生包含許多短序列(SAGE tag)的SAGE樣本,並且利用電腦工具輔以進行全面性之基因表現分析。但是由於現有之分析平台多缺乏一個良好且具備生物意義的方式來進行分析與比較,因此使其應用面大為受限;非但如此,在多樣本之分析與比較上仍有很大之挑戰空間,特別是在探勘腫瘤專一標記之情況。
在本研究中,我們從NCBI的GEO收集人類之各種SAGE樣本,並開發一個能夠有效探勘基因表現資料的分析軟體。本軟體提供了一個友善的操作介面,以協助使用者便利地進行操作與分析。我們開發了數個分析功能以供運用,使用者不但能夠同時對多個組織樣本進行交叉比較與分析且探勘基因之調控資訊,亦可以追蹤特定之基因於指定樣本中之表現情況,還可快速地查詢各種SAGE tag所對應之基因名稱與資訊。本軟體能夠有效協助生物學者們從多樣本之研究中,迅速發現不同組織特有之向上或向下調控標記,並且得知這些調控標記中哪些基因為專一的或者共通的,這對轉錄體之研究而言是非常重要且符合成本效益的。
Serial Analysis of Gene Expression is a powerful method that allows the analysis of complete gene expression patterns with computer-aided digital analysis. SAGE libraries are available in NCBI, NCI-CGAP and others databases for paralleled comparison on-line. However, visualization platforms for SAGE data still do not provide results of the SAGE data analysis in a convenient manner for cross-analysis and -comparison, thus limiting the application of the SAGE data. Furthermore, multiple-library comparisons among SAGE libraries are also challenging, especially for mining of tissue-specific gene candidates. In this study, we retrieved various SAGE libraries of Homo sapiens data from GEO and developed an effective software for analyzing SAGE data. The proposed software not only allows cross-analyzing and -comparing of the expression of various genes and mining of the regulative information among different SAGE libraries of tissue sources, but also provides the corresponding information between SAGE tags and genes of interest. Moreover, function to query SAGE tags of interest in selected SAGE libraries is also offered. To our knowledge, this is the first time that a user-friendly platform for cross-analysis and comparison of different SAGE libraries is offered. Some up- or down-regulated tissue-specific markers which are unique or common to others can be identified computationally. This is very important and convenient for conducting transcriptomic studies in silico in a cost-effective manner.
中文摘要
英文摘要
致謝
目錄
表目錄
圖目錄
一、緒論
1.1 介紹
1.2 研究動機
1.3 相關文獻探討
1.4 研究目的
1.5 論文架構
二、研究方法
2.1 數學集合論
2.1.1 樣本與樣本間之基因篩選
2.1.2 基因集合與基因集合間之篩選
2.2 階層式分群演算法
2.2.1 資料項目間之相似度量測
2.2.2 群集間之相似度量測方式
2.2.3 SAGE基因表現資料之分群
三、系統架構與設計
3.1 系統資料庫
3.2 輸入模組
3.3 矩陣資料產生器模組
3.4 交叉萃取模組
3.5 基因比對模組
3.6 基因追蹤模組
3.7 輸出模組
四、實驗結果與討論
4.1 產生基因表現矩陣檔案
4.2 探勘組織專一或共通標記
4.3 比對基因
4.4 追蹤基因表現
4.5 功能比較與總結
五、結論
六、未來研究
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