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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 歐陽彥正(Yen-Jen Oyang) | |
dc.contributor.author | Kai-Wei Liu | en |
dc.contributor.author | 劉凱維 | zh_TW |
dc.date.accessioned | 2021-06-08T07:14:51Z | - |
dc.date.copyright | 2008-08-06 | |
dc.date.issued | 2008 | |
dc.date.submitted | 2008-07-28 | |
dc.identifier.citation | 1. Lee, T.I., et al., Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 2002. 298(5594): p. 799-804.
2. Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104. 3. Barrera, L.O. and B. Ren, The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol, 2006. 18(3): p. 291-8. 4. Berman, H.M., et al., The Protein Data Bank. Nucleic Acids Res, 2000. 28(1): p. 235-42. 5. Ahmad, S. and A. Sarai, PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics, 2005. 6: p. 33. 6. Wang, L. and S.J. Brown, BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res, 2006. 34(Web Server issue): p. W243-8. 7. Yan, C., et al., Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 2006. 7: p. 262. 8. Fujii, Y., et al., Structural basis for the diversity of DNA recognition by bZIP transcription factors. Nat Struct Biol, 2000. 7(10): p. 889-93. 9. Watson, J.D., Molecular biology of the gene. 6th ed. 2008, San Francisco, CA.: Pearson. xxxii, 841 p. 10. Weaver, R.F., Molecular biology. 4th ed. 2008, Boston, Mass.: McGraw-Hill Higher Education. xxii, 890 29 cm. 11. Wasserman, W.W. and A. Sandelin, Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet, 2004. 5(4): p. 276-87. 12. TFBS, http://tfbs.genereg.net/DOC/TFBS/Matrix/PFM.html. 13. Matthews, B.W., Protein-DNA interaction. No code for recognition. Nature, 1988. 335(6188): p. 294-5. 14. Mandel-Gutfreund, Y., O. Schueler, and H. Margalit, Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J Mol Biol, 1995. 253(2): p. 370-82. 15. Pabo, C.O. and L. Nekludova, Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol, 2000. 301(3): p. 597-624. 16. Kono, H. and A. Sarai, Structure-based prediction of DNA target sites by regulatory proteins. Proteins, 1999. 35(1): p. 114-31. 17. Luscombe, N.M., et al., An overview of the structures of protein-DNA complexes. Genome Biol, 2000. 1(1): p. REVIEWS001. 18. Donald, J.E. and E.I. Shakhnovich, Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucleic Acids Res, 2005. 33(14): p. 4455-65. 19. Morozov, A.V. and E.D. Siggia, Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A, 2007. 104(17): p. 7068-73. 20. Sarai, A. and H. Kono, Protein-DNA recognition patterns and predictions. Annu Rev Biophys Biomol Struct, 2005. 34: p. 379-98. 21. Finn, R.D., et al., The Pfam protein families database. Nucleic Acids Res, 2008. 36(Database issue): p. D281-8. 22. Thompson, J.D., D.G. Higgins, and T.J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 1994. 22(22): p. 4673-80. 23. Chen, C.Y., et al., Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci U S A, 2008. 105(7): p. 2527-32. 24. Smith, T.F. and M.S. Waterman, Identification of common molecular subsequences. J Mol Biol, 1981. 147(1): p. 195-7. 25. Marabotti, A., et al., Energy-based prediction of amino acid-nucleotide base recognition. J Comput Chem, 2008. 26. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/. 27. Kielbasa, S.M., D. Gonze, and H. Herzel, Measuring similarities between transcription factor binding sites. BMC Bioinformatics, 2005. 6: p. 237. 28. Schones, D.E., P. Sumazin, and M.Q. Zhang, Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics, 2005. 21(3): p. 307-13. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/26551 | - |
dc.description.abstract | 轉錄因子在基因調控中扮演著重要的角色,能夠促進或抑制基因的表現。轉錄因子會與特定的DNA序列鍵結並發生作用,這個被鍵結的DNA區段稱為轉錄因子結合位置(TFBS)。然而,目前轉錄因子與基因間的互動網絡大部分仍屬未知,因此找出轉錄因子在DNA結合區上的關鍵殘基,能夠提供生化學家有用的訊息,設計實驗來確認轉錄因子與基因間的作用關係。當找出DNA結合區上的關鍵殘基後,我們就能進一步建立轉錄因子與DNA間結合模序的對應關係。而本篇論文的研究,即在於設計出一套方法達成上述的目標。這套方法是將DNA結合區類型相同的轉錄因子作TFBS的分群,接著從分群好的TFBS,在其對應DNA結合區的序列上,使用非常嚴苛的標準作多重序列排比,以找出DNA結合區上的關鍵殘基。我們也針對一些在蛋白質資料庫(PDB)中擁有三級結構資訊的轉錄因子,分析這套方法找出的關鍵殘基在物理化學上之重要性。 | zh_TW |
dc.description.abstract | Transcription factors (TFs) play an essential role in gene regulation by activating or inhibiting the expressions of the corresponding genes. The transcription factors carry out their functions by docking at a specific region in the DNA sequence, which is normally referred to as transcription factor binding site (TFBS). Since the complete network of the interactions between TFs and genes is still largely unknown, figuring out the key residues in the DNA binding domain of a TF can provide the biochemists with valuable information for design of biochemical experiments to verify the interactions between the TF and the corresponding genes. Furthermore, with the key residues in the DNA binding domain identified, we can move to establish a mapping between the DNA binding motifs and the TFBS motifs. In the study reported in this thesis, we have proposed a novel approach to achieve the objectives mentioned above. The proposed approach begins with clustering the TFBSs with the same binding type. Then, sequence alignment with a strict criterion is applied to the corresponding DNA binding domains of the TFBSs in the same cluster in order to identify the key residues in the DNA binding domains. For those TFs whose tertiary structure is present in the Protein Data Bank (PDB), we have examined the physiochemical significance of the key residues identified. | en |
dc.description.provenance | Made available in DSpace on 2021-06-08T07:14:51Z (GMT). No. of bitstreams: 1 ntu-97-R95922019-1.pdf: 779011 bytes, checksum: a82acd88bf7cd90800ee73d01e40ba93 (MD5) Previous issue date: 2008 | en |
dc.description.tableofcontents | 誌謝 Ⅰ
摘要 Ⅱ Abstract Ⅲ 目錄 Ⅳ 圖目錄 Ⅵ 表目錄 Ⅶ 第一章 緒論 1 1.1 背景 1 1.2 研究動機 1 1.3 章節說明 2 第二章 相關研究 3 2.1 轉錄因子 3 2.1.1 轉錄因子的種類 4 2.1.2 轉錄因子的功能區塊 4 2.1.3 轉錄因子結合位置 7 2.1.4 轉錄因子與DNA間的專一性結合 8 2.2 Pfam資料庫 9 2.3 分群演算法介紹 9 2.4 多重序列排比工具 10 第三章 研究方法 11 3.1 實驗目標 11 3.2 資料集 12 3.3 DNA結合區類型分群 13 3.4 相似度分數 14 3.4.1 Smith Waterman Alignment and Scoring 14 3.4.2 Gapped TFBS Alignment and Scoring 16 3.5 分群演算法 23 3.6 多重序列排比 24 第四章 實驗結果與討論 25 4.1 Zn_clus的實驗與結果 26 4.2 bZip的實驗與結果 30 4.3 Zf-C2H2的實驗與結果 34 4.4 HLH的實驗與結果 37 4.5 Myb的實驗與結果 40 第五章 結論與展望 43 5.1 結論 43 5.2 展望 44 參考文獻 45 | |
dc.language.iso | zh-TW | |
dc.title | 轉錄因子與DNA間結合模序對應關係之研究 | zh_TW |
dc.title | Mapping of Transcription Factor Binding Sites and DNA-Binding Motifs | en |
dc.type | Thesis | |
dc.date.schoolyear | 96-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 陳倩瑜(Chien-Yu Chen),蔡懷寬(Huai-Kuang Tsai),張天豪(Tien-Hao Chang) | |
dc.subject.keyword | 轉錄因子結合位置,DNA結合模序,PFM分群, | zh_TW |
dc.subject.keyword | TFBS,DNA-binding motif,PFM clustering, | en |
dc.relation.page | 45 | |
dc.rights.note | 未授權 | |
dc.date.accepted | 2008-07-30 | |
dc.contributor.author-college | 電機資訊學院 | zh_TW |
dc.contributor.author-dept | 資訊工程學研究所 | zh_TW |
顯示於系所單位: | 資訊工程學系 |
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