Abstract
Identifying and analyzing components of complexes is essential to understand the activities and organization of the cell. Moreover, it provides additional information on the possible function of proteins involved in these complexes. Two bioinformatics approaches are usually used for this purpose. The first is based on the identification, by clustering algorithms, of full or densely connected sub-graphs in protein—protein interaction networks derived from experimental sources that might represent complexes. The second approach consists of the integration of genomic and proteomic data by using Bayesian networks or decision trees. This approach is based on the hypothesis that proteins involved in a complex usually share common properties.
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References
Gavin, A. C., Bosche, M., Krause, R., et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147.
Ho, Y., Gruhler, A., Heilbut, A., et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183.
Butland, G., Peregrin-Alvarez, J. M., Li, J., et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537.
Veraksa, A., Bauer, A., Artavanis-Tsakonas, S. (2005) Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry. Dev Dyn 232, 827–834.
Mann, M., Hendrickson, R. C., Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 70, 437–473.
Rives, A. W., Galitski, T. (2003) Modular organization of cellular networks. Proc Natl Acad Sci U S A 100, 1128–1133.
Spirin, V., Mirny, L. A. (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100, 12123–1218.
Bader, G. D., Hogue, C. W. (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2.
Bu, D., Zhao, Y., Cai, L., et al. (2003) Top-ological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res 31, 2443–2450.
Asthana, S., King, O. D., Gibbons, F. D., et al. (2004) Predicting protein complex membership using probabilistic network reliability. Genome Res 14, 1170–1175.
Jansen, R., Lan, N., Qian, J., et al. (2002) Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics 2, 71–81.
Jansen, R., Yu, H., Greenbaum, D., et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302, 449–453.
Zhang, L. V., Wong, S. L., King, O. D., et al. (2004) Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5, 38.
Jansen, R., Greenbaum, D., Gerstein, M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res 12, 37–46.
Alfarano, C., Andrade, C. E., Anthony, K., et al. (2005) The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 33, D418–424.
Salwinski, L., Miller, C. S., Smith, A. J., et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32, D449–451.
Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., et al. (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res 32, D452–455.
Mewes, H. W., Frishman, D., Guldener, U., et al. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 30, 31–34.
Ball, C. A., Awad, I. A., Demeter, J., et al. (2005) The Stanford Micro-array Database accommodates additional micro-array platforms and data formats. Nucleic Acids Res 33, D580–582.
Iragne, F., Barre, A., Goffard, N., et al. (2004) AliasServer: a web server to handle multiple aliases used to refer to proteins. Bioinformatics 20, 2331–2332.
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© 2008 Humana Press, a part of Springer Science+Business Media, LLC
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Goffard, N., Weiller, G. (2008). Identifying Components of Complexes. In: Keith, J.M. (eds) Bioinformatics. Methods in Molecular Biology™, vol 453. Humana Press. https://doi.org/10.1007/978-1-60327-429-6_13
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DOI: https://doi.org/10.1007/978-1-60327-429-6_13
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