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Nucleic Acids Research 2006 34(Database Issue):D568-D571; doi:10.1093/nar/gkj074
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Nucleic Acids Research, 2006, Vol. 34, Database issue D568-D571
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context

Andreas Ruepp1,*, Octave Noubibou Doudieu1, Jos van den Oever1, Barbara Brauner1, Irmtraud Dunger-Kaltenbach1, Gisela Fobo1, Goar Frishman1, Corinna Montrone1, Christine Skornia1, Steffi Wanka1, Thomas Rattei2, Philipp Pagel1,2, Louise Riley1, Dmitrij Frishman2, Dimitrij Surmeli1, Igor V. Tetko1, Matthias Oesterheld1, Volker Stümpflen1 and H. Werner Mewes1,2

1Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany 2Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science D-85350 Freising-Weihenstephan, Germany

*To whom correspondence should be addressed. Tel: +49 89 3187 3189; Fax: +49 89 3187 3585; Email: andreas.ruepp{at}gsf.de

Received August 15, 2005. Revised October 8, 2005. Accepted October 8, 2005.

MfunGD (http://mips.gsf.de/genre/proj/mfungd/) provides a resource for annotated mouse proteins and their occurrence in protein networks. Manual annotation concentrates on proteins which are found to interact physically with other proteins. Accordingly, manually curated information from a protein–protein interaction database (MPPI) and a database of mammalian protein complexes is interconnected with MfunGD. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme which is widely used for the analysis of protein networks. The dataset is also supplemented with information about the literature that was used in the annotation process as well as links to the SIMAP Fasta database, the Pedant protein analysis system and cross-references to external resources. Proteins that so far were not manually inspected are annotated automatically by a graphical probabilistic model and/or superparamagnetic clustering. The database is continuously expanding to include the rapidly growing amount of functional information about gene products from mouse. MfunGD is implemented in GenRE, a J2EE-based component-oriented multi-tier architecture following the separation of concern principle.


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