簡易檢索 / 詳目顯示

回結果列表
研究生： 林俞君
Yu-Chun Lin
論文名稱： A Robust Network Alignment Algorithm for Detecting Evolutionarily Conserved Protein Complexes Across Species
利用強健式網路比對演算法來找尋跨物種演化間共同的蛋白質複合體
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 - 資訊系統與應用研究所
Institute of Information Systems and Applications
論文出版年： 2008
畢業學年度： 96
語文別： 英文
論文頁數： 40
中文關鍵詞： 網路比對 、蛋白質複合體 、蛋白質網路 、生物知識本體論語意相似度
外文關鍵詞： Network alignment, Protein complexes, Protein networks, Ontology based semantic similarity
相關次數： 點閱：4  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

    • 由於生物網路結構相當的複雜，從現今的圖形化軟體來呈現生物網路並且去從中擷取出跨物種間共同的網路結構是一件相當困難的事情，因此，如何利用電腦的快速搜尋與網路比對方式比較不同的生物網路來挖掘分析共同的網路結構，尤其是探討在不同物種間具有相似功能的群聚式蛋白質複合體是值得研究的議題。首先，我們結合生物基因序列相似比對分析的工具以及生物知識本體論的語意相似程度來找到可能的跨物種間的相似蛋白質，進而將她們群聚起來再利用深度優先搜尋法，進行相似網路比對以找尋共同的網路結構。由於生物演化過程中可能會產生基因複製與生物網路結構性的轉變，因此我們的方法在比對生物網路的過程中允許結構上的小差異，而不是只單純找到跨物種間完全相同網路。我們利用小型的無向圖、有向圖和四個大型生物蛋白質網路(釀酒酵母、秀麗隱桿線蟲、幽門螺旋桿菌及大腸桿菌)來做為我們的測試資料，並且比較之前所提出過網路比較方法，依據我們的方式可以找尋到跨物種間更多共同的網路結構，我們也利用現今釀酒酵母正確的蛋白質複合體來驗證，實驗結果也顯示我們有較高的準確率與涵蓋率，而且電腦搜尋所需花費的時間也不會以指數型的方式增加。透過我們的方式未來能進一步來預測人類生物體中未知的蛋白質複合體，讓人類的生物網路的藍圖能夠更加明確。

    中文摘要 I Abstract III Acknowledgement IV List of Figures V List of Tables VI 1. INTRODUCTION 1 1.1 Molecular Networks 1 1.2 Evolution of Networks 2 1.3 Conservation Studies 3 1.4 Related Works 3 1.5 Organization of the thesis 6 2. METHODS 7 2.1  Network alignment problem 8 2.1.1 Formulation of network alignments  8 2.1.2 Definitions of matches and mismatches 9 2.2 Nodes clustering based on similarity score 10 2.3  Depth-first search for network alignments 14 2.4  Significant testing based on the accumulative hyper-geometric distributions 16 2.5  Statistical validation of the alignments 18 2.6  Materials 19 3. EXPERIMENTS AND RESULTS 20 3.1 Multi-alignment of undirected networks 20 3.2 Aligning directed networks 22 3.3 A case analysis of our results 23 3.4 Comparisons with MaWish and DivAfull 33 4. DISCUSSION AND CONCLUSION 36 REFERENCES 37

    Ashburner M, et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25: 25-29.
    Bader GD, et al. (2001) BIND – The biomolecular interaction network database. Nucleic Acids Res., 29: 242-245.
    Barabasi AL, et al. (2004) Network biology: understanding the cell’s functional organization. Nat. Rev. Genet., 5: 101-113.
    Benjamini, Yoav and Hochberg, Yosef. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 57(1): 289-300.
    Berg,J. et al. (2004) Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol.Biol., 4, 51.
    Diana Ekman, et al. (2006) What properties characterize the hub proteins of the protein-protein interaction network of saccharomyces cerevisiae? Genome Biology, 7(6): R45.
    Ellison. V. and Stillman. (2003) Biochemical Characterization of DNA Damage Checkpoint Complexes: Clamp Loader and Clamp Complexes with Specificity for 5' Recessed DNA. PloS , 1 (2 ), 1-13
    H. W. Mews, et al. (1998) MIPS: a database for protein sequences and complete genomes, Nucleic Acids Research, 1998, Vol. 26, No. 1 33–37
    Ioannis Xenarios, et al. (2002) Dip, the database of interacting proteins: a search tool for studying cellular networks of protein interactions. Nucleic Acids Research, 30(1): 303-305.
    Jason Flannick, et al. (2006) Graemlin: General and robust alignment of multiple large interaction networks, Genome Res., 2006 16: 1169-1181.
    Kelly,B.P et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl Acad. Sci. USA., 100, 11394-11399.
    Kelly,B.P et al. (2004) PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res., 32, 83-88.
    Koyuturk,M., et al. (2005) Pairwise local alignment of protein interaction network guided by modes of evolution. RECOMB 2005, LNBI, 3500, 48-65.
    Koyuturk,M., et al. (2006) Pairwise alignment of protein interaction networks. J. Comput. Biol., 13(2): 182-199.
    Maslov.S and Sneppen,K (2002) Specificity and stability in topology of protein networks. Science, 296, 910-913
    Pavol Jancura, et al. (2008) Divide, Align and Full-Search for Discovering Conserved Protein Complexes. EVOBIO.2008
    Pengjun Pei; et al. (2007) A “Seed-Refine” Algorithm for Detecting Protein Complexes From Protein Interaction DataNanoBioscience, IEEE Transactions on Volume 6, Issue 1, Page(s):43 - 50
    Przulj,N. (2005) Knowledge Discovery in Proteomics: Graph Theory Analysis of Protein-Protein Interactions. CRC Press.
    P.W. Lord (2003) Semantic Similarity Measures as Tools for Exploring the Gene Ontology, Pacific Symposium on Biocomputing 8:601-612
    Rohit Singh, et al., (2007) Global alignment of multiple protein interaction networks. RECOMB.
    Sharan,R., et al. (2005) Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci., 102: 1974-1979.
    Sharan,R., et al. (2005) Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J. Comput. Biol., 12(6): 835-846.
    Sharan,R. and Ideker,T. (2006) Modeling cellular machinery through biological network comparison. Nat. Biotechnol., 24, 427-433.
    S. H. Yook, et. al (2004) Role of the Cytoskeleton in Signaling Network",. J. Cell Sci. 117, 2769
    Wanger,A. (2001) The yeast protein interaction networks evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol., 18, 1283-1292.
    Zhenping Li, et al. (2007) Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23, 1631-1639.
    Zhi Liang, et al. (2006) Comparison of protein interaction networks reveals species conservation and divergence. BMC Bioinformatics 2006, 7:457

    無法下載圖示 全文公開日期 本全文未授權公開 (校內網路)
    全文公開日期 本全文未授權公開 (校外網路)

    QR CODE