跳到主要內容

臺灣博碩士論文加值系統

(3.236.84.188) 您好!臺灣時間:2021/08/06 10:25
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

: 
twitterline
研究生:陳毅誠
研究生(外文):Yi-Cheng Chen
論文名稱:運用探索式資料分析找尋蛋白質磷酸化鄰近區域之特定樣本
論文名稱(外文):Identification of protein phosphorylation motifs through exploratory data analysis
指導教授:鍾翊方
指導教授(外文):I-Fang Chung
學位類別:碩士
校院名稱:國立陽明大學
系所名稱:生物醫學資訊研究所
學門:工程學門
學類:生醫工程學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:英文
論文頁數:55
中文關鍵詞:序列單元磷酸化作用K-均值法機器學習
外文關鍵詞:MotifPhosphorylationk-meansmachine learning
相關次數:
  • 被引用被引用:0
  • 點閱點閱:202
  • 評分評分:
  • 下載下載:23
  • 收藏至我的研究室書目清單書目收藏:0
我們發展了一個叫做F-Motif的新方法來進行磷酸化motifs鑑定。這個獨特的方法運用了非監督式的分群技術將用數值特徵表示的序列資料進行探索隱含在訓練資料中的統計資訊。我們已將數個新的以及既有的資料運用來比較我們和另一個眾所皆知的方法(Motif-X)的效果。F-Motif的結果可以辨認出所有Motif-X找到的motifs,並且還能發現更多新的motifs。我們同時也藉由文獻探討展示了那些新找到的motifs的確是沒有被發現過的。
We have developed a novel unsupervised method for identification of phosphorylation motifs, called F-Motif. This is a unique method that uses clustering of sequence information represented by numerical features that exploit the statistical information hidden in the training data. We have applied the proposed method on several new and existing data sets and compared its performance with a well known method (Motif-X) in the literature. The F-Motif is found to identify all motifs identified by Motif-X. In addition to this, F-Motif discovers some novel motifs. We have demonstrated using clues from the literature that these new motifs found by F-Motif are indeed novel.
Chinese Abstract I
English Abstract II
Table of Contents III
List of Figures IV
List of Tables V
Chapter 1: Introduction 1
1.1 Background 1
1.2 Related work 4
1.3 Motivation and specific aim 5
Chapter 2: Materials and methods 7
2.1 Data sets 7
2.1.1 Foreground data sets 8
2.1.2 Background data sets 10
2.2 Motif finding algorithm 11
2.2.1 Step 1: Encoding of sequence data 12
2.2.2 Step 2: Clustering and finding of potential and candidate motifs 14
2.2.3 Step 3: Motif set generation 19
Chapter 3: Results and discussions 23
3.1 Motif discovery result 23
3.2 Robustness with respect to encoding of data 28
3.3 The influence of threshold T 30
3.4 Novel motifs identified by F-Motif 31
Chapter 4: Conclusion and future work 51
Reference 53
[1] Abel, A., Fonknechten, N., Hofer, A., Durr, A., Cruaud, C., Voit, T., Weissenbach, J., Brice, A., Klimpe, S., Auburger, G., and Hazan, J. Early onset autosomal dominant spastic paraplegia caused by novel mutations in SPG3A. Neurogenetics, 5(4):239-243 (2004).
[2] Albuquerque, C.P., Smolka, M.B., Payne, S.H., Bafna, V., Eng, J., and Zhou, H. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics, 7(7):1389-1396 (2008).
[3] Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S.G., Pandey, A. A curated compendium of phosphorylation motifs. Nat Biotechnol, 25(3):285-286 (2007).
[4] Bailey, T.L. and Elkan, C. The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol, 3:21-29 (1995).
[5] Balla, S., Thapar, V., Verma, S., Luong, T., Faghri, T., Huang, C.H., Rajasekaran, S., del Campo, J.J.,Shinn, J.H., Mohler, W.A., Maciejewski, M.W., Gryk, M.R., Piccirillo, B., Schiller, S.R., Schiller, M.R. Minimotif Miner: a tool for investigating protein function. Nat Methods, 3(3):175–177 (2006).
[6] Beausoleil, S.A., Jedrychowski, M., Schwartz, D., Elias, J.E., Villén, J., Li, J., Cohn, M.A., Cantley, L.C., and Gygi, S.P. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci USA, 101(33):12130–12135 (2004).
[7] Bezdek, J.C. Pattern recognition with fuzzy objective function algorithms. New York: Plenum (1981).
[8] Blom, N., Sicheritz-Pontén, T., Gupta, R., Gammeltoft, S., and Brunak, S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics, 4(6):1633-1649 (2004).
[9] Boucher, L.M., Marengere, L.E., Lu, Y., Thukral, S., and Mak, T.W. Binding sites of cytoplasmic effectors TRAF1, 2, and 3 on CD30 and other members of the TNF receptor superfamily. Biochem Biophys Res Commun, 233(3):592-600 (1997).
[10] Claverie, J.M. and Audic, S. The statistical significance of nucleotide position-weight matrix matches. Comput Appl Biosci, 12(5):431-439 (1996).
[11] Cross, T.G., Scheel-Toellner, D., Henriquez, N.V., Deacon, E., Salmon, M., and Lord, J.M. Serine/threonine protein kinases and apoptosis. Exp Cell Res, 256(1):34-41 (2000).
[12] Das, M.K. and Dai, H.K. A survey of DNA motif finding algorithms. BMC Bioinformatics, 8(Suppl 7):S21 (2007).
[13] Diella, F., Gould, C.M., Chica, C., Via, A., and Gibson, T.J. Phospho.ELM: a database of phosphorylation sites—update 2008. Nucleic Acids Res, 36(Database issue):D240-D244 (2008).
[14] Gnad, F., Ren, S., Cox, J., Olsen, J.V., Macek, B., Oroshi, M., and Mann, M. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol, 8(11):R250 (2007).
[15] Huang, H.D., Lee, T.Y., Tzeng, S.W., and Horng, J.T. KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res, 33:W226-W229 (2005).
[16] Jonassen, I., Collins, J.F., and Higgins, D.G. Finding flexible patterns in unaligned protein sequences. Protein Sci, 4(8):1587-1595 (1995).
[17] Manning, G., Whyte, D.B., Martinez, R., Hunter, T., Sudarsanam, S. The protein kinase complement of the human genome. Science, 298(5600):1912-34 (2002).
[18] Neuberger, G., Schneider, G., and Eisenhaber, F. pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. Biol Direct, 2:1 (2007).
[19] Nishida, K., Frith, M.C., and Nakai, K. Pseudocounts for transcription factor binding sites. Nucleic Acids Res, 37(3):939-944, (2009).
[20] Obenauer, J.C., Cantley, L.C., and Yaffe, M.B. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res, 31(13):3635–3641 (2003).
[21] Pawson, T. and Scott, J.D. Protein phosphorylation in signaling—50 years and counting. Trends Biochem Sci, 30(6):286-290 (2005).
[22] Pinna, L.A. and Ruzzene, M. How do protein kinases recognize their substrates? Biochim Biophys Acta, 1314(3):191-225 (1996).
[23] Qiu, P., Cai, X.Y., Wang, L., Greene, J.R., and Malcolm, B. Hepatitis C virus whole genome position weight matrix and robust primer design. BMC Microbiol, 2:29 (2002).
[24] Rigoutsos, I. and Floratos, A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics, 14(1):55-67 (1998).
[25] Ritz, A., Shakhnarovich, G., Salomon, A.R., and Raphael, B.J. Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinformatics, 25(1):14-21 (2009).
[26] Roig, J., Tuazon, P.T., Zipfel, P.A., Pendergast, A.M., and Traugh, J.A. Functional interaction between c-Abl and the p21-activated protein kinase gamma-PAK. Proc Natl Acad Sci USA, 97(26):14346-14351 (2000).
[27] Rothe, M., Wong, S.C., Henzel, W.J., and Goeddel, D.V. A novel family of putative signal transducers associated with the cytoplasmic domain of the 75 kDa tumor necrosis factor receptor. Cell, 78(4):681-692 (1994).
[28] Schwartz, D. and Gygi, S.P. An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol, 23(11):1391-1398 (2005).
[29] Schwartz, D., Chou, M.F., and Church, G.M. Predicting protein post-translational modifications using meta-analysis of proteome-scale data sets. Mol Cell Proteomics, 8(2):365-379 (2009).
[30] Sugiyama, N., Nakagami, H., Mochida, K., Daudi, A., Tomita, M., Shirasu, K., and Ishihama, Y. Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol, 4:193 (2008).
[31] Tuazon, P.T., Spanos, W.C., Gump, E.L., Monnig, C.A., and Traugh, J.A. Determinants for substrate phosphorylation by p21-activated protein kinase gamma-PAK. Biochemistry, 36:16059-16064 (1997).
[32] Wan, J., Kang, S., Tang, C., Yan, J., Ren, Y., Liu, J., Gao, X., Banerjee, A., Ellis, L.B., and Li, T. Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection. Nucleic Acids Res, 36(4):e22 (2008).
[33] Winston, L.A. and Hunter, T. Intracellular signalling: putting JAKs on the kinase MAP. Curr Biol, 6(6):668-671 (1996).
[34] Yoo, P.D., Ho, Y.S., Zhou, B.B., and Zomaya, A.Y. SiteSeek: post-translational modification analysis using adaptive locality-effective kernel methods and new profiles. BMC Bioinformatics, 9:272 (2008).
[35] Zhai, B., Villén, J., Beausoleil, S.A., Mintseris, J., and Gygi, S.P. Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res, 7(4):1675-1682 (2008).
[36] Crooks, G.E., Hon, G., Chandonia, J.M., Brenner, S.E. WebLogo: A sequence logo generator. Genome Research, 14:1188-1190(2004).
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top