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研究生: 張永謚
Chang, Yung-I
論文名稱: 建立在酵母菌中與砷反應相關基因之資料庫
Construction of a Database of Yeast Arsenic-Related Genes
指導教授: 吳謂勝
Wu, Wei-Sheng
學位類別: 碩士
Master
系所名稱: 電機資訊學院 - 電機工程學系
Department of Electrical Engineering
論文出版年: 2017
畢業學年度: 105
語文別: 中文
論文頁數: 46
中文關鍵詞: 表型篩選基因表現分析
外文關鍵詞: arsenic, phenotypic screening, transcriptional profiling
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  • 砷是目前普遍存在的類金屬元素,當吸收高濃度的無機砷時會讓人得到皮膚癌、肝癌、膀胱癌、肺癌還有烏腳病等,這對人體的健康影響非常的大,所以我們要找出解決的方法。目前的生物學家利用兩種實驗(例如表型篩選和基因表現分析)得到了酵母菌中許多砷相關的基因,這些砷相關的基因是對於代謝砷毒性非常重要的關鍵,但是它們目前分散於許多文獻中,想要研究的人還要一一去尋找文獻,無法快速得知,這也引發我們開發了YARG(酵母菌對抗砷相關資訊)資料庫,其中我們於NCBI中得到了9篇砷相關基因,而這些文獻是利用了兩種實驗技術來做分類,最後整合了3416個砷相關的基因,對於每個基因提供了實驗數據和類型(表型篩選或基因表現分析)。使用者可以根據搜索或瀏覽模式查詢,在搜尋模式中使用者可以用兩種方法搜尋分別是(i)輸入單一基因,主要是得到這個基因是否與砷有相關,也可以連結到SGD和YeastMine得取更多砷相關的資訊。(ii)輸入一群基因,主要是讓使用者知道這群基因到底跟砷相關性是否高,也可以藉由圖表看出在各個實驗技術出現的證據數。在瀏覽模式中使用者可以選擇三種,分別是(i)根據自己想查看的染色體去點選,此功能就是讓使用者知道我們的3416基因到底在第幾條染色體占大多數。(ii)根據表型篩選技術去查看,此功能提供了3416個基因到底有哪幾群基因是用表型篩選得到的,也可以知道它們來自哪篇文獻以及它們的實驗條件。(iii)根據基因表現分析技術去查看,此功能提供了3416個基因到底有哪幾群基因是用基因表現分析得到的,也可以知道它們來自哪篇文獻以及它們的實驗條件。而我們使用了yap1來證明出YARG可以提供許多有用的連結以及證據。也用了2008年Serero等人用鎘研究出一群砷敏感型的基因,我們利用它們來與YARG資料庫做比對,最後得到了它們與我們3416個砷相關的基因重疊率很高,此證明了砷和鎘可能會有相同的代謝路徑。YARG希望提供給想研究砷的學者更便利的做研究,YARG資料庫目前可在下列網址取得http://cosbi4.ee.ncku.edu.tw/YARG/。

    Arsenic is currently the prevalence of metal-like elements, when the absorption of high concentrations of inorganic arsenic will make people get skin cancer, liver cancer, bladder cancer, lung cancer and black foot disease. Which the health of the human body is very big, so we need to find a solution. Current biologists use two experiments (such as phenotypic screening and Transcriptional Profiling) to obtain many arsenic-related genes in yeast which are critical to metabolic arsenic toxicity, but they are currently dispersed in many of the literature, the people who want to study and find the literature, can’t quickly know which also led us to develop the YARG (Yeast Arsenic-Related Genes) database, which we got nine arsenic Related genes in NCBI, which use two experimental techniques to classify, final we integration 3416 arsenic-related genes, providing experimental data and type (phenotypic screening or Transcriptional Profiling) for each gene. User can according to search mode or browse mode to search.In search mode user can (i) input a gene and get result . (ii) input a list of genes and get result. In browse mode user can (i)select 3416 arsenic-related genes by chromosomes. (ii)select 13 arsenic-related gene lists generated by phenotypic screening. (iii) select 7 arsenic-related gene lists generated by transcriptional profiling. We use yap1 to prove that the link provided by YARG is useful. And also used cadmium to develop a group of arsenic-sensitive genes in 2008 Serero et al. We use the list of genes to against the YARG database then we find that it have high rate similar with our 3416 arsenic-related genes. It’s prove they may ha ve same metabolic pathways. Final YARG can provide scholar more convenient to do research .The web is available online at http://cosbi4.ee.ncku.edu.tw/YARG/.

    目錄 中文摘要 i 英文摘要 iii 致謝 vii 表目錄 x 圖目錄 xi 英文縮寫對照 xii 第一章 研究背景與動機 1 1 1.1 砷的概要 1 1.2 酵母菌作為砷的研究系統 2 1.3 表現型篩選-基因表現分析 4 1.4 與砷研究相關的資料庫 7 1.5 動機 10 1.6 論文架構 11 第二章 資料來源與方法 13 2.1 資料蒐集 13 2.2 資料前處理 21 第三章 結果與討論 25 3.1 資料庫功能與介面介紹 25 3.1.1 搜尋頁(Search mode) 26 3.1.2 瀏覽模式(Browse mode) 33 第四章 實例探討 39 第五章 結論與未來展望 44 5.1 結論 44 5.2 未來與展望 45 參考文獻 46

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    [8] Thorsen, M., et al., Genetic basis of arsenite and cadmium tolerance in Saccharomyces cerevisiae. BMC Genomics, p. 105, 2009.
    [9] Jo, W.J., et al., Comparative functional genomic analysis identifies distinct and overlapping sets of genes required for resistance to monomethylarsonous acid (MMAIII) and arsenite (AsIII) in yeast. Toxicol Sci, p. 424-36, 2009.
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