簡易檢索 / 詳目顯示
| 研究生： |
卓文福 Wen-Fu Cho |
|---|---|
| 論文名稱： |
應用資料採礦於基因體之重複序列資料庫 Data Mining for Regulatory Elements in Repeat Sequences |
| 指導教授： |
洪炯宗
Jorng-Tzong Horng |
| 口試委員: | |
| 學位類別： |
碩士 Master |
| 系所名稱： |
資訊電機學院 - 資訊工程學系 Department of Computer Science & Information Engineering |
| 畢業學年度： | 88 |
| 語文別： | 中文 |
| 論文頁數： | 38 |
| 中文關鍵詞： | 轉錄因子資料庫 、轉錄因子 、關聯性規則 、資料採礦 、重複序列 、基因組序列 |
| 外文關鍵詞： | Repeat Sequences, TRANSFAC, Transcription Factor, Association Rule, Data Mining, Genome Sequence |
| 相關次數： | 點閱：10 下載：0 |
| 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 |
自人類基因計畫推行以來，各種大規模基因體定序技術高度發展，已知DNA序列數目大幅增加，這些基因中包含很多重覆出現的序列(Repeat Sequence)。重複序列在醫藥診斷和研究扮演重要的角色。目前已發展一個完整儲存重覆序列的資料庫，將提供國內生物資訊研究者研究及使用，將存放所有生物基因體中有重覆的序列。轉錄因子資料庫存放很多轉錄因子，本文標記轉錄因子於重複序列，應用資料採礦(Data Mining)的關聯性(Association Rule)技術於重複序列中轉錄因子的組合。我們將發現的關聯性規則找出較有意義的，並且去除多餘的規則，並應用關聯性對基因體中的重覆序列進行部份分類(Partial Classification)。我們進行的實驗包含人類第二十二條基因體及其它基因體。在面對生物基因體的研究上，將使我們得到相當有價值的資訊。
Human Genome Project began at 1988 and then lots of genomes will be sequencialized later. Repeat sequences in genome sequences play an important role in medical diagnosis and research. The Transcription factor database TRANSFAC collects many promoter classes. In this thesis, we first mark the transcription factor binding sites in the repeat sequences and then apply data mining techniques to mine the association rules from the combinations of binding sites. We further prune the discovered associations to remove those insignificant associations and find a set of useful rules. Finally, we use the discovered association rules to partially classify the repeat sequences in our repeat database. We also experiment on several genomes including C.Elegans, Human Chromosome 22, and Yeast.
[1] T.Heinemeyer, X.Chen, H.Karas, A. E.Kel, O. V.Kel, I.Liebich, T.Meinhardt, I.Reuter, F.Schacherer and E.Wingender, "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms". Nucleic Acids Research 27, 318-322 (1999).
[2] T.Heinemeyer, E. Wingender, I. Reuter, H. Hermjakob, A. E. Kel, O. V. Kel, E. V. Ignatieva, E. A. Ananko, O. A. Podkolodnaya, F. A. Kolpakov, N. L. Podkolodny and N. A. Kolchanov, "Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL", Nucleic Acids Research, 362-367(1998).
[3] A. Brazma, J. Vilo, E. Ukkonen and K. Valtonen, "Data Mining for Regulatory Elements in Yeast Genome". In ''Proceedings of the Fifth International Conference Intelligent Systems for Molecular Biology'', AAAI Press, 65-74 (1997).
[4] A. Brazma, J. Vilo and E. Ukkonen, "Finding Transcription Factor Binding Site Combinations in Yeast Genome (Extended Abstract) ". Computer Science and Biology, Proceedings of the German Conference on Bioinformatics. Frishman and H.W. Mewes (ed.), 57-59 (1997).
[5] R. Agrawal and R. Srikant, "Fast Algorithms for Mining Association Rules'', Proceedings of the 20th Int''l Conference on Very Large Databases, Santiago, Chile, Sept. 1994. Expanded version available as IBM Research Report RJ9839, 487-499(1994).
[6] R. Agrawal, T. Imielinski and A. Swami, "Mining Associations between Sets of Items in Large Databases'', Proceedings of the ACM SIGMOD Int''l Conference on Management of Data, Washington D.C., 207-216 (1993).
[7] R. Srikant and R. Agrawal, "Mining Generalized Association Rules", Proc. of the 21st Int''l Conference on Very Large Databases, Zurich, Switzerland, Sep. 1995. Expanded version available as IBM Research Report RJ 9963, 407-419(1995).
[8] B. Kero, L. Russell, S. Tsur and W.M. Shen, "An Overview of Database Mining Techniques". KDOOD/ TDOOD, 1-8(1995).
[9] R. Srikant, Q. Vu and R. Agrawal, "Mining Association Rules with Item Constraints". Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 67-73(1997).
[10] R. Srikant, Q. Vu and R. Agrawal, "Mining Association Rules with Item Constraints". Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining: 67-73(1997).
[11] K. Ali, S. Manganaris and R. Srikant, "Partial Classification Using Association Rules". Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 115-118(1997).
[12] B. Liu, W. Hsu and Y. Ma, "Pruning and Summarizing the Discovered Associations", Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 125-134 (1999).
[13] M. Klemettinen, H. Mannila and H. Toivonen, "A Data Mining Methodology and Its Application to Semi-automatic Knowledge Acquisition". Database and Expert Systems Applications Workshop, 670-677(1997).
[14] H. Toivonen, M. Klemettinen, P. Ronkainen, K. Hatonen, and H. Mannila, "Pruning and grouping discovered association rules". In MLnet Workshop on Statistics, Machine Learning, and Discovery in Databases, Heraklion, Crete, Greece, 47-52 (1995).
[15] M. Klemettinen, H. Mannila, P. Ronkainen, H. Toivonen and A. Inkeri Verkamo, "Finding Interesting Rules from Large Sets of Discovered Association Rules". Proceedings of the 1994 ACM CIKM International Conference on Information and Knowledge Management, 401-407(1994).
