簡易檢索 / 詳目顯示

研究生: 徐崇瀚
Chung-Han Hsu
論文名稱: 應用卵巢癌微陣列資料建構基因調控網路之研究
Construction of Gene Regulation Networks from Ovarian Cancer Microarray Data
指導教授: 蘇順豐
Shun-Feng, Su
口試委員: 蔡超人
Chau-Ren, Tsai
王偉彥
"none"
鄭錦聰
"none"
莊鎮嘉
"none"
學位類別: 碩士
Master
系所名稱: 電資學院 - 電機工程系
Department of Electrical Engineering
論文出版年: 2007
畢業學年度: 95
語文別: 英文
論文頁數: 88
中文關鍵詞: 卵巢癌基因調控網路基因晶片
外文關鍵詞: Ovarian cancer, Gene regulation networks, Gene chip
相關次數: 點閱:173下載:1
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報
  • 在生物資訊這個領域中,基因調控網路佔有著非常重要的地位。在生物資訊傳輸路徑系統中,基因調控網路記載著蛋白質之間的生物化學反應,因此,可以提供詳細且重要的資訊以提供研究人員作更進一步的調查與分析。了解基因調控網路的重要性,我們將研究重點放在卵巢癌的基因調控網路之建立。其卵巢癌基因的取得是由虎尾科技大學的鄭錦聰教授所提供。我們使用Ariadne 公司所研發的Pathway Studio這套軟體。透過使用這套軟體,順利的建立了這些基因的調控網路。一些可能的卵巢癌基因被輸入至這套軟體而得到相關的基因調控網路。透過這樣有系統的分析,我們發現如果掌握了最重要的基因,就可以確實地調控其他的基因並影響整個基因調控網路系統。此外,經過基因篩選,我們能更容易的理解基因之間的調控關係並且能更容易的發現最重要的基因。我們希望能提供後續研究的一些相關基礎並期許能得到更進一步的結果或是更為寬廣的應用。


    In the field of biology information, gene regulation networks play a very important role. In the system of biology information transduction pathway, gene regulation networks record the biochemical event between proteins. Thus, it can provide detailed and important information so that researchers can have decent investigation and analysis. In view of the importance of gene regulation networks, we focused our research on the construction of gene regulation networks for ovarian cancer. The gene data of ovary cancer is provided by Professor Jeng of National Formosa University. We use the software, Pathway Studio (Ariadne Company’s products). With the use of the software, these gene regulation networks are constructed. Several possible key genes for Ovary cancer are defined and feed into the software to obtain their related gene regulation network. Through this arrangement and systematic analysis, we find if command the most important gene, it can certainly regulation other genes and influence whole network. Besides, after sieve, we can easily realize the relationship of gene regulation and easily find the most important gene.We wish to provide bases for follow-up research and to obtain more depth fruitful results or to have more broadly applications.

    Contents 摘要……………………………………………………………..I Abstract………………………………………………………...II 誌謝…………………………………………………………...III Contents……………………………………………………….IV List of Tables…………………………………………………VII List of Figures……………………………………………….VIII Chapter 1 Introduction 1.1 Research motivation and background ----------------------------------1 1.2 Thesis Organization -------------------------------------------------------2 Chapter 2 Related Knowledge 2.1 Ovary Cancer --------------------------------------------------------------4 2.1.1 About Ovary Cancer--------------------------------------------------------------4 2.1.2 The pathogenesis reason----------------------------------------------------------4 2.1.3 Classification and 5 Years Survival Rate--------------------------------------5 2.1.4 Condition----------------------------------------------------------------------------5 2.1.5 Surgical Stages----------------------------------------------------------------------6 2.2 Biochip ---------------------------------------------------------------------7 2.3 Bioinformatics -----------------------------------------------------------15 2.4 Gene Regulation Networks (Pathway) --------------------------------18 2.5 DNA and RNA summary -----------------------------------------------19 2.5.1 Nucleic acids ----------------------------------------------------------------------19 2.5.2 What is DNA? --------------------------------------------------------------------22 2.5.3 DNA ‘s structure -----------------------------------------------------------------24 2.5.4 DNA ‘s character -----------------------------------------------------------------26 2.5.5 Compare with DNA and RNA -------------------------------------------------27 2.5.6 RNA’s classification -------------------------------------------------------------28 Chapter 3 Literature review 3.1 Experiment information source introduction ------------------------29 3.1.1 Introduction bioinformatics database ---------------------------------------29 3.1.2 The classical principle of Gene ontology (GO) -----------------------------33 3.2 Introduce to complicate network ----------------------------------------34 3.3 Gene network’s principle ------------------------------------------------37 3.3.1 Gene network’s basic characteristic -------------------------------------------38 3.3.2 Gene network’s application -----------------------------------------------------39 3.3.3 GRNs research’s mainly contents ----------------------------------------------39 3.4 Gene regulation network’s research method ---------------------------41 3.4.1 Mainly method ---------------------------------------------------------------------41 3.4.2 Basic network unit ----------------------------------------------------------------42 3.5 Biochip technology application in gene’s express --------------------43 3.5.1 Biochip’s manufacture -----------------------------------------------------------45 3.5.2 Biochip’s inspection --------------------------------------------------------------48 3.5.3 Data’s statistics analysis ---------------------------------------------------------48 Chapter 4 Experiment process and method 4.1 Introduction by Pathway Studio -----------------------------------------51 4.2 Using this software to construction GRNs -----------------------------52 Chapter 5 Ovary cancer’s GRNs result 5.1 Down-regulated genes in ovarian tumor/cancer ----------------------62 5.2 The 12 gene markers obtained -------------------------------------------70 5.3 Genes over - expressed at early stage of ovarian cancer -------------75 Chapter 6 Conclusion and Outlook 6.1 Contribution and conclusion ---------------------------------------------81 6.2 Suggest and outlook ------------------------------------------------------82 Reference --------------------------------------------------------------83 作者簡介…………………………………………………….. 87 授權書………………………………………………………...88

    Reference

    [1] Bristow, R.E. and Karlan B.Y., “Ovulation induction, infertility, and ovarian cancer risk,” Fertil. Steril., Vol.66, No.4, pp. 499-507(1996).
    [2] Venn A., Watson L., Lumley J., Giles G., King C., and Healy D., “Breast and ovarian cancer incidence after infertility and in vitro fertilization,” Lancet., Vol.346, No.8981, pp.995-1000(1995).
    [3] Rossing M.A., Daling J.R., Weiss N.S., Moore D.E., and Self S.G., “Ovarian tumors in a cohort of infertile women,” N. Engl. J. Med., Vol.331, No.12, 771-6(1994).
    [4] Standards, options and recommendations: clinical practice guidelines for cancer care from the French National Federation of Cancer (FNCLCC). Ovarian cancer. Bri. J. Cancer., Vol.84, pp.18-23(2001).
    [5] FIGO staging classifications and clinical practice guidelines in the management of gynecologic cancers. Int. J. Gynecol. Obstet., Vol.70, pp.209-262(2000).
    [6] Shepherd, J.H., Revised FIGO staging for gynaecological cancer. Br. J. Obstet. Gynaecol., Vol.96, No.8, pp.889-92(1989).
    [7] 工業技術研究院生技醫藥所: http://www.bmec.itri.org.tw/default.asp
    [8] 楊永楠, 「可攜帶型快速診斷感染性疾病基因晶片光電系統之研發」, 國立東華大學電機工程研究所碩士論文,2004年。
    [9] 莊慧明,「生物晶片. 產業調查與技術」,第141期,第 2-25頁,2001年。
    [10] 張維懋,「生物晶片研發概況」,科學月刊, 第三十三卷, 第9期, 第716-719頁, 1999年9月。
    [11] 張儀賢,「低操作電壓之數位微流體進樣傳輸晶片及其在聚合酶連鎖反應之應用」,國立成功大學工程科學研究所碩士論文,2004年。
    [12] Ferré and R.A. Gibbs, “The Polymerase Chain Reaction,” Birkhäuser, 1994.
    [13] 李國賓,「下一波之生物晶片-微流體生醫晶片之應用及研發」, 科學發展月刊, 第385期, 第73-77頁,2005年。
    [14] 王政光等編著、王雯靜總校閱(2002),「生物資訊」,九州出版社,臺北。
    [15] Parry-Smith, and David J,“Introduction to bioinformatics,” Prentice Hall,1999.
    [16] 盧信智,「應用卵巢癌之微陣列晶片分析基因表現量及調控路徑」,國立台灣科技大學電機工程研究所碩士論文,2005年。
    [17] 三浦謹一郎著(1984)、劉文政譯,「DNA與遺傳訊息」,國立編譯館,臺北。
    [18] 德利卡(Karl A. Drlica)著、周業仁譯(2003),「DNA的十四堂課」,天下遠見出版,大和圖書總經銷,臺北。
    [19] 林正焜、洪火樹著(2005),「認識DNA:下一波的醫療革命」,商周出版,家庭傳媒城邦分公司發行,臺北。
    [20] 生命的螺旋 : http://biotech.nstm.gov.tw/01/011.asp
    [21] 維基百科 : http://zh.wikipedia.org/wiki/DNA
    [22] 國家科學委員會網站 : http://biotech.nsc.gov.tw/7-02.html
    [23] 生物化學基礎 : http://juang.bst.ntu.edu.tw/BCbasics/index.htm
    [24] GenomeNet (http://www.genome.ad.jp/).
    [25] Kanehisa Laboratory (http://kanehisa.kuicr.kyoto-u.ac.jp).
    [26] Kanehisa,M.,“A database for post-genome analysis,” Trends Genet.,Vol.13, pp.375-376(1997).
    [27] KEGG (http://www.genome.ad.jp/).
    [27] Kanehisa, M. and Goto, S., “KEGG: Kyoto Encyclopedia of Genes and Genomes,” Nucleic Acids Res, Vol.28, pp.27-30(2000).
    [28] 洪堃斌,「透過GenNav及KEGG資料庫設計疾病相關信息路徑的快速搜尋機制」,國立台灣科技大學電機工程研究所論文(2004)。
    [29] 徐俊皓,「以基因本體論為基礎用隱含關鍵字搜尋PubMed資料庫」,國立雲林科技大學電子與資訊工程研究所論文(2005)。
    [30] 王文宏,「利用一個以基因本體論為基礎之語意相似度量測來發掘相似功能之基因」,國立成功大學資訊工程學系碩博士班論文(2004)。
    [31] 吳金閃,狄增如,「從統計物理學看複雜網路研究」,物理學進展,第24期,第19-46頁(2004)。
    [32] Albert, R. and Barabási, “A-L. Statistical mechanics of complex networks,” Rev. Mod. Phys. Vol.74, pp.47–97(2000).
    [33] Narat J. Eungdamrong, Ravi Iyengar. “Modeling Cell Signaling Networks,” Biology of theCell, Vol.96, pp.355-362.
    [34] 陳美榮教授上課講義,「複雜網路簡介與基本概念」,香港城市大學。
    [35] Thieffry D.,"From global expression data to gene networks, "Bioessays, Vol.21, No.11, pp.895-899(1999).
    [36] Dassow G., Meir E., Munro E. M.,et., "The segment polarity network is a robust development module, "Nature, Vol.406, No.13, pp.188-192(2000).
    [37] Wagner A., " Robustness against mutations in genetic networks ofyeast, "Nature Genetics, Vol.4, No.4, pp.355-361(2000).
    [38] Blaiseau P. L., Thomas D.Multiple, " transcriptional activation complexes tether the yeast activator Met4 to DNA, "EMBOJournal , Vol.17, No.21, pp.6327-6336(1998).
    [39] Gemma Swiers, Roger Patient, Matthew Loose, "Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification, " Developmental Biology, Vol.294, pp.525-540(2006).
    [40] Holstege F., Jennins E., Wyrick J., et al, "Dissecting the regulatory circuity of a eukaryotic genome, "cell, Vol.95, pp.717-728(1998).
    [41] Iyer V., Eisen M., Ross D., et al, "The transcriptional program in the response of human fibroblasts to serum, "Science, Vol.283, pp.83-87(1999).
    [42] 馬立人、蔣中華、白壽雄,「生物晶片」,臺北,九州圖書(2003)。
    [43] 李國賓,「微流體生物晶片」,科學發展第385期,第72~77(2005)。
    [44] 毛彥傑、王維漢、陳來勝,「生物晶片市場與技術概況」,機械工業雜誌第267 期,第47~54(2005)。
    [45] Affymetrix: http://www.affymetrix.com/index.affx
    [46] Pathway Studio使用手冊
    [47] Ariadne Genomics,Inc (http://www.ariadnegenomics.com/)

    QR CODE