MPact: the MIPS protein interaction resource on yeast
Ulrich Güldener,Martin Münsterkötter,Matthias Oesterheld,Philipp Pagel,Andreas Ruepp,Hans-Werner Mewes,Volker Stümpflen +6 more
TLDR
The implementation of a web-based PPI-analysis tool allows analysis and visualization of protein interaction networks and facilitates integration of curated data with high-throughput datasets.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. 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 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.read more
Citations
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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk,Andrea Franceschini,Michael Kuhn,Milan Simonovic,Alexander Roth,Pablo Minguez,Tobias Doerks,Manuel Stark,Jean Muller,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information.
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The IntAct molecular interaction database in 2012
Samuel Kerrien,Bruno Aranda,Lionel Breuza,Alan Bridge,Fiona Broackes-Carter,Carol Chen,Margaret Duesbury,Marine Dumousseau,M Feuermann,Ursula Hinz,Christine Jandrasits,Rafael C. Jimenez,Jyoti Khadake,Usha Mahadevan,Patrick Masson,Ivo Pedruzzi,Eric Pfeiffenberger,Pablo Porras,Arathi Raghunath,Bernd Roechert,Sandra Orchard,Henning Hermjakob +21 more
TL;DR: Two levels of curation are now available within the IntAct database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported.
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CORUM: the comprehensive resource of mammalian protein complexes—2009
Andreas Ruepp,Brigitte Waegele,Martin Lechner,Barbara Brauner,Irmtraud Dunger-Kaltenbach,Gisela Fobo,Goar Frishman,Corinna Montrone,H. Werner Mewes +8 more
TL;DR: A ‘Phylogenetic Conservation’ analysis tool was implemented that analyses the potential occurrence of orthologous protein complex subunits in mammals and other selected groups of organisms and allows one to predict the occurrence of protein complexes in different phylogenetic groups.
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MINT: a Molecular INTeraction database.
Andreas Zanzoni,Luisa Montecchi-Palazzi,Michele Quondam,Gabriele Ausiello,Manuela Helmer-Citterich,Gianni Cesareni +5 more
TL;DR: MINT, a database designed to store data on functional interactions between proteins, consists of entries extracted from the scientific literature by expert curators assisted by ‘MINT Assistant’, a software that targets abstracts containing interaction information and presents them to the curator in a user‐friendly format.
Journal ArticleDOI
MINT: the Molecular INTeraction database
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TL;DR: MINT, a database designed to store data on functional interactions between proteins, consists of entries extracted from the scientific literature by expert curators assisted by 'MINT Assistant', a software that targets abstracts containing interaction information and presents them to the curator in a user-friendly format.
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