(3.237.20.246) 您好!臺灣時間:2021/04/17 15:21
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果

詳目顯示:::

我願授權國圖
: 
twitterline
研究生:溫國政
研究生(外文):Kuo-Cheng Wen
論文名稱:癌症相關基因探勘與預測
論文名稱(外文):An Integrated System for Cancer-Related Genes Mining and Prediction
指導教授:陳士農陳士農引用關係
指導教授(外文):Shih-Nung Chen
學位類別:碩士
校院名稱:亞洲大學
系所名稱:資訊工程學系碩士班
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:2005
畢業學年度:94
語文別:中文
論文頁數:142
中文關鍵詞:癌症相關基因異型接合性損失比較型基因組雜交法資料探勘選擇性剪接序列樣本
外文關鍵詞:cancer-related gene(loss of heterozygosityLOHcomparative genomic hybridizationCGHdata miningalternative splicingpattern
相關次數:
  • 被引用被引用:0
  • 點閱點閱:170
  • 評分評分:系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
根據統計在已開發國家和開發中國家,癌症發生率機率高,可以說是人類健康的敵人,一般人在一生中罹患癌症的機率是四分之一,隨著生態環境的破壞,生活習慣和飲食習慣的改變,癌症罹患率每年不斷的上升,因此對癌症發生原因的研究是相當重要的課題,但是醫學研究人員在取得醫學文獻時卻遇到資訊過量的問題,再加上要從大量的資訊當中以人工方式取出重要資訊,不但浪費時間也容易造成錯誤。本研究的目標是發展一平台來整合、收集、分析以及預測癌症相關基因(cancer-related gene)的資訊。本論文我們利用NCBI的PubMed搜尋引擎來搜尋癌症相關基因的醫學文獻(medical literature)與序列(sequence),根據使用者輸入的癌症名稱和LOH (loss of heterozygosity)或CGH (comparative genomic hybridization)做組合進行文獻的收集、分類、以及探勘,在癌症相關基因預測的部份,利用選擇性剪接(alternative splicing)的特性區分各正常組織與不正常組織的各種選擇性剪接表現型態,並且找出選擇性剪接表現形式以及特殊的序列樣本(pattern)。本論文提出的方法能夠探勘出重要資訊以及能了解各組織的特性,能加快醫學研究人員的研究並可節省許多時間,另外也可以將此方法應用到其他疾病上。
According to statistics, the rate of having cancer is relatively high for people in developing and developed countries. So cancer can be called as the enemy of human health. With the destruction of ecological environment and with the change of life style and diet, the rate of having cancer during the life of a general individual is one and a quarter and grows continuously by year. Thus, it is important to study the cause of cancer. However, while biomedical researchers search and retrieve biomedical literature, there is a problem of information overloading. Therefore, to survey thousands and hundreds of biomedical literatures by manual browsing is time wasting and difficult to make sure whether required information can be found. Besides, artificial inattention may lead to incorrect analysis information. The purpose of this study is to develop an integrated system for collecting,mining cancer-related gene and prediction cancer-related gene. This system uses PubMed search engine of NCBI to search and retrieve biomedical literature and sequence of cancer-related gene. Users can combine cancer name and LOH (loss of heterozygosity), or cancer name and CGH (comparative genomic hybridization) to search, retrieve, collect, classify, and extract the biomedical literatures.This system use character of alternative splicing to search for alternative splicing forms and sequences patterns. This system can extract important information to accelerate the study and save plenty of time for biomedical researchers. Besides, this system can also be used on other diseases
摘要 i
Abstract ii
目錄 iii
圖目錄 vi
表目錄 viii
表目錄 viii
第一章 緒論 1
1.1研究背景 1
1.2研究動機 2
1.3研究目的 3
1.4研究方法 3
1.5研究架構 4
第二章 相關研究 5
2.1生物相關研究 5
2.1.1 中心法則 5
2.1.2 RNA剪接(splicing) 6
2.1.3選擇性剪接(Alternative splicing) 7
2.1.4 SR蛋白質(Serine/arginine-rich protein) 9
2.1.5基因體雜交比較法(Comparative Genomic Hybridization,CGH)與異型接合缺失(Loss of Heterozygosity,LOH) 10
2.2醫學文獻探勘 11
2.3選擇性剪接 13
2.4資料庫 15
2.4.1 MeSH 15
2.4.2 PubMed 16
2.4.3 Entrez Gene 17
2.4.4 RefSeq 18
2.4.5 Ensembl 19
2.4.6 GeneCards 20
第三章 研究架構 21
3.1 研究流程 21
3.2 系統架構 22
3.4資料來源收集 24
3.4.1癌症相關資訊收集 24
3.4.2基因相關資訊收集 25
3.4.3基因序列收集 27
3.4.4相關醫學文獻收集 30
3.5醫學文獻的探勘 32
3.6分類選擇性剪接之序列 35
3.7選擇性剪接之表現形式 36
3.8選擇性剪接序列樣本 38
第四章 實作與結果 41
4.1癌症相關基因探勘 41
4.2選擇性剪接之表現形式 45
4.3特殊序列樣本 54
4.4結合SR蛋白之序列樣本 62
第五章 結論與未來研究方向 66
5.1結論 66
5.2未來研究方向 67
參考文獻 68
附錄A 癌症資訊 71
附錄B 基因組織分類 75
附錄C 二維關聯分析 79
附錄D 選擇性剪接表現形式 85
附錄E 特殊序列樣本 91
附錄F 結合SR蛋白之序列樣本 97
附錄G 論文發表 107
誌 謝 132
簡 歷 133
[1]行政院衛生署, 93年臺灣地區主要死因分析,http://www.doh.gov.tw/。
[2]蘇武雄, 癌症, 臺北市:水牛, 1991。
[3]F. Crick, “Central Dogma of Molecular Biology,” Nature, vol. 227, pp. 561-563 Aug. 1970.
[4]基因定序核心實驗室, http://www.cgmh.com.tw/intr/intr2/c32a0/chinese/。
[5]終身網路學習教材_生物科技面面觀, http://biotech.nstm.gov.tw/home.asp。
[6]B. Modrek and C. Lee “A genomic view of alternative splicing,” Nature Genetics, vol. 30, no.1, pp.13-19, 2002.
[7]J. R. Sanford and J. F. Caceres, “Pre-mRNA splicing: life at the centre of the central dogma,” Journal of Cell Science, vol. 117, no.26, pp. 6261-6263, Dec.2004.
[8]L. Cartegni, S. L. Chew and A. R. Krainer , “Listening to silence and understanding nonsense: exonic mutations that affect splicing,” 2002 Nature Publishing Group, vol. 3, pp. 285-298, April 2002.
[9]D. Brett, J. Hanke, G. Lehmann, S. Haase, S. Delbru«ck, S. Krueger, J. Reich and P. Bork, “EST comparison indicates 38% of human mRNAs contain possible alternative splice forms,” FEBS Letters, vol. 474, no. 1, pp. 83-86, May 2000.
[10]E. Y. Levanon and R. Sorek, “The importance of alternative splicing in the drug discovery process,” TARGETS, vol. 2, no. 3, pp. 109-114, June 2003.
[11]C. W. J. Smith and J. Valcárcel, "Alternative pre-mRNA splicing: the logic of combinatorial control," Trends in biochemical sciences, vol. 25, no. 8, pp.381-388, Aug. 2000.
[12]A. Kallioniemi, O. P.Kallioniemi, D. Sudar, D.Rutovitz, J. W. Gray, F. Waldman and D. Pinkel, “Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors,” Science, vol. 258, no. 5083, pp.818-21, Oct. 1992.
[13]S. H. Bigner, M. R. Matthews, B. K. A. Rasheed, R. N. Wiltshire, H. S. Friedman, A. H. Friedman, T. T. Stenzel, D. M. Dawes, R. E. McLendon, and D. D. Bigner, “Molecular Genetic Aspects of Oligodendrogliomas Including Analysis by Comparative Genomic Hybridization,” American Journal of Pathology, vol. 155, no. 2, pp.375-368, Aug. 1999.
[14]C. A. Klein, O. Schmidt-Kittler, J. A. Schardt, K. Pantel, M. R. Speicher and G. Riethmulier, “Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells,” in Proceedings of the National Academy of Sciences of the United States of America ,vol. 96, no. 8, pp. 4494-4499, April 1999.
[15]N. Wong, P. Lai, S. W. Lee, S. Fan, E. Pang, C. T. Liew, Z. Sheng, J. W. Y. Lau and P. J. Johnson “Assessment of Genetic Changes in Hepatocellular Carcinoma by Comparative Genomic Hybridization Analysis,” American Journal of Pathology, vol. 154, no. 1, Jan. 1999.
[16]S. Joos, B. Schütz, M. Bentz, and P. Lichter, ”Detection of chromosomal imbalances using DOP-PCR and comparative genomic hybridization (CGH),” Nonradioactive in situ Hybridization Application Manual, pp. 95-103, 2002.
[17]A. Koike, Y. Niwa and T. Takagi, “Automatic extraction of gene/protein biological functions from biomedical text,” Bioinformatics, vol. 21, no. 7, pp. 1227-1236, 2005.
[18]R. Homayouni, K. Heinrich, L. Wei and M. W. Berry, “Gene clustering by latent semantic indexing of MEDLINE abstracts,” Bioinformatics, vol. 21, pp. 104-115, 2005.
[19]Z. Z. Hu, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker and C. H. Wu , “Literature mining and database annotation of protein phosphorylation using a rule-based system,” Bioinformatics, vol. 21, pp. 2759-2765, June 2005.
[20]Y. Liu, S. B. Navathe, J. Civera, V. Dasigi, A. Ram, B. J. Ciliax, and R. Dingledine, “Text mining biomedical literature for discovering gene-to-gene relationships: a comparative study of algorithms,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 1, pp. 62-76, Jan. 2005.
[21]N. Uramoto, H. Matsuzawa, T. Nagano, A. Murakami, H. Takeuchi and K. Takeda, “A text-mining system for knowledge discovery from biomedical documents,” IBM Systems Journal, vol. 43, no. 3, pp. 516-533, July 2004.
[22]Q. Xu, B. Modrek and C. Lee “Genome-wide detection of tissue specific alternative splicing in human transcriptome,” Nucleic Acids Research, vol. 30, no. 17, pp. 3754-3766, Sep. 2002.
[23]S. Boue, M. Vingron, E. Kriventseva and I. Koch, “Theoretical analysis of alternative splice forms using computational methods,” Bioinformatics, vol. 18, pp.s65-s73, 2002.
[24]Y. Lian and H. R. Garner “Evidence for the regulation of alternative splicing via complementary DNA sequence repeats,” Bioinformatics, vol. 21 no. 8, pp. 1358-1364, 2005
[25]Z. Wang, H. S. Lo, H. Yang, S. Gere, Y. Hu, K. H. Buetow, and M. P. Lee “Computational Analysis and Experimental Validation of Tumor-associated Alternative RNA Splicing in Human Cancer,” Cancer Research, pp. 655-657, Feb. 2003.
[26]MeSH, http://www.nlm.nih.gov/mesh/MBrowser.html。
[27]PubMed, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed。
[28]K. D. Pruitt and D. R. Maglott, “RefSeq and LocusLink: NCBI gene-centered resources,” Nucleic Acids Research, vol. 29, no. 1, pp.137-140, 2001.
[29]D. Maglott, J. Ostell, K. D. Pruitt and T. Tatusova, “Entrez Gene: gene-centered information at NCBI,” Nucleic Acids Research, vol. 33, pp. D54-D58, 2005.
[30]Entrez Gene ,http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene。
[31]RefSeq, http://www.ncbi.nlm.nih.gov/projects/RefSeq/。
[32]Ensembl, http://www.ensembl.org/Homo_sapiens/index.html。
[33]E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, et. al., “Ensembl 2006,” Nucleic Acids Research, vol. 34, pp. D556-D561, 2006.
[34]GeneCards, http://www.genecards.org/index.shtml。
[35]M. Rebhan, V. Chalifa-Caspi, J. Prilusky and D. lancet “GeneCards:a novel functional genomics compendium with automated data minin and query reformulation support,” Bioinformatics, vol.14, no. 8, pp.656-664, 1998.
[36]R. H. Guttman, A. G. Moukas, and P. Maes, “Agent-mediated electronic commerce: a survey,” The Knowledge Engineering Review archive, vol. 13, no. 2, pp.147-159, July 1998.
[37]S. Franklin and A. Graesser, “Is it an agent, or just a program?: a taxonomy for autonomous agents,” in Proceedings of the Third International Workshop on Agent Theories, Architectures, and Languages, 1996, pp. 21-35.
[38]G. Salton and C. Buckley, "Term-weighting approaches in automatic text retrieval," Information Processing and Management, Vol. 24, No. 5, pp. 513-523, 1988.
[39]C. Lee, L. Atanelov, B. Modrek and Y. Xing, “ASAP: the Alternative Splicing Annotation Project,” Nucleic Acids Research, vol. 31, no. 1, pp. 101-105, 2003.
[40]T. A. Thanaraj, S. Stamm, F. Clark, Jean-Jack Riethoven, V. L. Texier and J. Muilu, “ASD: the Alternative Splicing Database,” Nucleic Acids Research, vol.32, pp.D64-D49, 2004.
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top
無相關期刊
 
系統版面圖檔 系統版面圖檔