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研究生:林俞君
研究生(外文):Yu-Chun Lin
論文名稱:ARobustNetworkAlignmentAlgorithmforDetectingEvolutionarilyConservedProteinComplexesAcrossSpecies
論文名稱(外文):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:蘇豐文蘇豐文引用關係
指導教授(外文):Von-Wun Soo
學位類別:碩士
校院名稱:國立清華大學
系所名稱:資訊系統與應用研究所
學門:電算機學門
學類:系統設計學類
論文種類:學術論文
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 alignmentProtein complexesProtein networksOntology based semantic similarity
相關次數:
  • 被引用被引用:0
  • 點閱點閱:253
  • 評分評分:
  • 下載下載:13
  • 收藏至我的研究室書目清單書目收藏:1
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
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