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研究生： 吳憲宗
Hsien-Tsung Wu
論文名稱： 用時間分割與時間平移方法比對微陣列時間序列資料來分析酵母菌細胞週期的基因互動
Analysis of Genetic Interactions in Yeast Cell-Cycle Using Time-split and Time-sliding Comparisons on Time-series Microarray Data
指導教授： 蘇豐文
Von-Wun Soo
口試委員:
學位類別： 碩士
Master
系所名稱： 電機資訊學院 - 資訊工程學系
Computer Science
論文出版年： 2008
畢業學年度： 96
語文別： 英文
論文頁數： 36
中文關鍵詞： 生物晶片 、基因調控網路
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    • 在生物資訊領域中，基因調控網路的推導是一項很重要的議題。雖然目前已經能夠用生物晶片來測量大量的基因表現，但基因之間的相互調控關係仍然尚未全部被了解。由於進行生物實驗必須消耗大量的時間、人力和物力，所以使用資訊科技來輔助基因調控網路的推導，將可為生物學家節省大量的成本。
    在本論文中，我們改變過去使用全段基因表現時間序列資料相似度比對的方法，改以切割的方式，取出在生物實驗過程中，基因實際相互影響的片段作為我們基因關聯性配對的依據，再根據基因反應延遲時間來推測可能的調控方向，最後完成基因調控網路的推導。因此我們的論文主要意旨可分為兩大部分：一、基因關聯性配對；二、基因調控方向推導。
    我們從史丹佛大學的酵母菌細胞週期計畫網頁上取得我們需要的基因表現時間序列資料，再採用我們所提出的方法進行實驗，最後根據文獻驗證我們所推導出的網路。實驗證明我們所提出的方法在使用相似度比對的方法上能有正面的助益。

    中文摘要……………………………………………………………………………iii Abstract………………………………………………………………………………iv Table of Contents…………………………………………………………………v Table of Figures…………………………………………………………………vi List of Tables……………………………………………………………………vii Chapter 1 Introduction………………………………………………………………1 11 Microarray technology……………………………………………………………1 12 The cell cycle……………………………………………………………………2 13 The gene expression………………………………………………………………3 14 The lagging time…………………………………………………………………4 15 Gene regulatory networks………………………………………………………4 16 Gene expression time series data…………………………………………………5 17 The correlation method……………………………………………………………5 18 Organization of the thesis…………………………………………………………6 Chapter 2 Related works……………………………………………………………7 21 Previous studies…………………………………………………………………7 22 Motivations………………………………………………………………………9 23 Objectives and contributions……………………………………………………10 Chapter 3 The methods………………………………………………………………12 31 Gene pair inference13 311 The correlation methods13 3111 The Spearman’s rank correlation method14 3112 Determining significance17 312 The time-split method18 3121 Equal division19 3122 To divide by searching19 323 Inferring the gene pairs by the time-split method20 33 Detecting direction of interaction using the time-sliding method21 331 The time-sliding method21 332 Determine the direction of interaction…………………………………………24 Chapter 4 The Experiments and Discussions………………………………………26 41 The experiment I…………………………………………………………………26 42 The experiment II………………………………………………………………27 43 The experiment III………………………………………………………………27 44 Comparisons……………………………………………………………………28 45 The Target Networks……………………………………………………………29 Chapter 5 Conclusions………………………………………………………………31 References……………………………………………………………………………32 Appendix I: Student's t-distribution…………………………………………………35

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    16. Yuh, C.-H., Bolouri, H., and Davidson, E., (1998) Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science 279, 1896–1902.
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