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NAR Molecular Biology Database Collection entry number 841
Gueldener U.1, Muensterkoetter M.1, Oesterheld M.1, Pagel P.1, Ruepp A.1, Mewes H.W.1,2 and Stuempflen V.1
1Institute for Bioinformatics, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
2Technische Universitaet Muenchen, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany

Database Description

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 relatedto the proximity of proteins in yeast. Besidethe 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. Guldener, G. Mannhaupt, M. Munsterkotter 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 anextensive 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


We thank Louise Riley, Gisela Fobo, Barbara Brauner, Goar Frishman, Corinna Montrone and Irmtraud Dunger for excellent annotation. This work was supported by a grant of the German Federal Ministry of Education and Research (BMBF) within theBFAM framework (031U112C/212C), the European Commission (QLRI-CT 1999-01333) and the Impuls- und Vernetzungsfonds der Helmholtz-Gemeinschaft Deutscher Forschungszentren eV.

Go to the abstract in the NAR 2006 Database Issue.
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