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. 2006 Jan 1;34(Database issue):D436-41.
doi: 10.1093/nar/gkj003.

MPact: the MIPS protein interaction resource on yeast

Ulrich Güldener  1 , Martin Münsterkötter, Matthias Oesterheld, Philipp Pagel, Andreas Ruepp, Hans-Werner Mewes, Volker Stümpflen
Affiliations

MPact: the MIPS protein interaction resource on yeast

Ulrich Güldener et al. Nucleic Acids Res. .

Abstract

In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein-protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been called a gold standard because of its quality and comprehensiveness [H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J. D. Han, N. Bertin, S. Chung, M. Vidal and M. Gerstein (2004) Genome Res., 14, 1107-1118]. MPact and the yeast protein localization catalog provide information related to the proximity of proteins in yeast. Beside the integration of high-throughput data, information about experimental evidence for PPIs in the literature was compiled by experts adding up to 4300 distinct PPIs connecting 1500 proteins in yeast. As the interaction data is a complementary part of CYGD, interactive mapping of data on other integrated data types such as the functional classification catalog [A. Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Güldener, G. Mannhaupt, M. Münsterkötter and H. W. Mewes (2004) Nucleic Acids Res., 32, 5539-5545] is possible. A survey of signaling proteins and comparison with pathway data from KEGG demonstrates that based on these manually annotated data only an extensive overview of the complexity of this functional network can be obtained in yeast. The implementation of a web-based PPI-analysis tool allows analysis and visualization of protein interaction networks and facilitates integration of our curated data with high-throughput datasets. The complete dataset as well as user-defined sub-networks can be retrieved easily in the standardized PSI-MI format. The resource can be accessed through http://mips.gsf.de/genre/proj/mpact.

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Figures

Figure 1
Figure 1
The GenRE n-tier architecture. JSP—JavaServer Pages; XML—Extensible Markup Language; XSL—Extensible Stylesheet Language; JDBC—Java DataBase Connectivity; CYGD—Comprehensive Yeast Genome Database; and FGDB—Fusarium graminearum Genome DataBase.
Figure 2
Figure 2
(A–C)Statistical analysis of the manually extracted data.
Figure 3
Figure 3
Interaction network of signal transduction proteins restricted to physical interactions, high-throughput interactions not included. Node colors indicate the most prevalent functional category assigned to all proteins of a sub-network.
See this image and copyright information in PMC

References

    1. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature. 2000;403:623–627. - PubMed
    1. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA. 2001;98:4569–4574. - PMC - PubMed
    1. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., Bork P. Comparative assessment of large-scale data sets of protein–protein interactions. Nature. 2002;417:399–403. - PubMed
    1. Jansen R., Yu H., Greenbaum D., Kluger Y., Krogan N.J., Chung S., Emili A., Snyder M., Greenblatt J.F., Gerstein M. A Bayesian networks approach for predicting protein–protein interactions from genomic data. Science. 2003;302:449–453. - PubMed
    1. Ge H., Liu Z.H., Church G.M., Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genet. 2001;29:482–486. - PubMed

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