了解蛋白質在細胞中所扮演的角色一直是生物學中一項很重要的課題。近年來，由於新的蛋白質交互作用偵測實驗技術相繼問世，例如yeast two-hybrid可以在一次實驗中產生出大量蛋白質交互作用的資料。有了這些大量的蛋白質交互作用資料，我們可以將這些資料轉化蛋白質交互作用網路。利用蛋白質交互作用網路來偵測必要性蛋白質。
在本篇論文中，我們提出一些特性分析的方法在蛋白質交互作用網路上偵測必要性蛋白質。我們觀察蛋白質與其鄰居所形成的鄰居間最大連通子以及鄰居間最大連通子圖的密度。我們認為必要性蛋白質在蛋白質交互作用網路上的鄰居間最大連通子圖大小會比非必要性蛋白質要來得大，且鄰居間最大連通子圖之間的關係會較緊密。我們的結果顯示，這種特性分析在蛋白質交互作用網路上偵測必要性蛋白質的偵測上能夠得到比前人更好的結果。

Determining protein function in the cells is one of the most important tasks in the post-genomic era. Recently, high-throughput experiments such as yeast two-hybrid could obtain large amounts of protein-protein interaction data. We can construct the protein-protein interaction network from these protein-protein interaction data, and detect essential protein from the protein-protein interaction network.
In this thesis, we first observe each protein’s maximum connected component from its neighborhood and density of the maximum component. We find that in general, an essential protein’s maximum component from its neighborhood is larger than that of a nonessential protein, and the density of maximum component from its neighborhood is denser as well. we present two approaches based on the above graph characteristics to detect essential proteins from the protein-protein interaction network. The results of our approaches are better than other earlier approaches.

Bader,G.D. and Hogue,C.W.V. (2002) Analyzing yeast protein–protein interaction data obtained from different sources. Nat Biotechnol., 20, 991–997.
Bu,D., Zhao,Y., Cai,L., Xue,H., Zhu,X., Lu,H., Zhang,J., Sun,S., Ling,L., Zhang,N., Li,G. and Chen,R. (2003) Topological structure analysis of the protein–protein interaction network in budding yeast. Nucleic Acids Res., 31, 2443–2450.
Chin,C.S. and Samanta,M.P. (2003) Global snapshot of a protein interaction network—a percolation based approach. Bioinformatics, 19, 2413-2419.
Criekinge,W.V. and Beyaert,R. (1999) Yeast two-hybrid: State of the art. BiolProced Online, 2, 1-38.
Deane,C.M., Salwinski,L., Xenarios,I. and Eisenberg,D. (2002) Protein interactions: two methods for assessment of the reliability of high throughput observations. Cell Proteomics, 1, 349–356.
Deng,M., Sun,F., and Chen,T. (2003) Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput, 140-151.
Egan,J. (1975) Signal Detection Theory and ROC Analysis, Academic Press, New York.
Estrada,E., (2006) Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics 2006, 6, 35–40.
Estrada,E. and Rodriguez-Velazquez,J.A., (2005) Subgraph centrality in complex networks. Physical Review E., 71, 056103.
Gagneur,J., Krause,R., Bouwmeester,T. and Casari,G., (2004) Modular decomposition of protein-protein interaction networks. Genome Biology, 5, R57.
Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141–147.
Giaever,G., Chu,A.M., Ni,L., Connelly,C., Riles,L., Ve´ronneau,S., et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387-391.
Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectroscopy. Nature, 415, 180–183.
Hyle,J.W., Randal,J.S. and Reines,D. (2003) Functional Distinctions between IMP Dehydrogenase Genes in Providing Mycophenolate Resistance and Guanine Prototrophy to Yeast. The Journal Of Biological Chemistry, 278, 31, 28470–28478.
Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Natl Acad. Sci. USA, 98, 4569–4574.
Jeong,H., Mason,S.P., Barabasi,A.L. and Oltvai,Z.N. (2001) Lethality and centrality in protein networks. Nature, 411, 41–42.
John,C.G. and Kaufman,P.D. (1999)Role of Saccharomyces cerevisiae Chromatin Assembly Factor-Iin Repair of Ultraviolet Radiation Damage in Vivo. Genetics 151, 485–497.
Liebler,D.C. (2002) Introduction to Proteomics-Tools for the New Biology. Humana Press Inc. New Jersey.
Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623–627.
Mangus,D.A., Amrani,N. and Jacobson,A. (1998) Pbp1p, a Factor Interacting with Saccharomyces cerevisiae Poly(A)-Binding Protein, Regulates Polyadenylation. Molecular and cellular biology, 18, 12, 7383-7396.
Pržulj,N., .Wigle,D.A. and Jurisica,I. (2003) Functional topology in a network of protein interactions. Bioinformatics, 20, 340-348.
Saito,R., Suzuki,H., and Hayashizaki,Y. (2003) Construction of reliable protein–protein interaction networks with a new interaction generality measure. Bioinformatics, 19, 756–763.
Saito,R., Suzuki,H., and Hayashizaki,Y. (2002) Interaction generality, a measurement to assess the reliability of a protein–protein interaction. Nucleic Acids Res., 30, 1163–1168.
Samanta,M.P., and Liang,S. (2003) Redundancies in large-scale protein interaction networks Proc. Natl Acad. Sci., 100, 12579–12583.
Smith,D., Gerstein,M., Reed,M.A. and Snyder,M. (2000) Analysis of yeast protein kinases using protein chips. Nat. Genet., 26, 283–289.
Sprinzak,E., Sattath,S. and Margalit,H. (2003) How reliable are experimental protein–protein interaction data? J. Mol. Biol., 327, 919–923.
Stauffer,D. and Aharony,A. (1994) Introduction to Percolation Theory. Taylor and Francis, London.
Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., et al. (2002) Specificity and stability in topology of protein networks. Science, 296, 910.
von Mering,C.V., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields S. and Bork P., (2002) Comparative assessment of largescale data sets of protein–protein interactions. Nature, 417, 399–403
Winzeler,E.A., Shoemaker,D.D., Astromoff,A., Liang,H., Keith Anderson,B., et al. (1999) Functional characterization of the Saccharomyces cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901–906.