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

By Andreas Ruepp, Octave Noubibou Doudieu, Jos van den Oever, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Christine Skornia, Steffi Wanka, Thomas Rattei, Philipp Pagel, Louise Riley, Dmitrij Frishman, Dimitrij Surmeli, Igor V. Tetko, Matthias Oesterheld, Volker Stümpflen and H. Werner Mewes

Abstract

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

Topics: Article
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:1347437
Provided by: PubMed Central
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    1. (2005). 100 InterPro, progress and status in 2005.
    2. 75 Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    3. (2004). Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network.
    4. (2004). Constructing free energy approximations and generalized belief propagation algorithms.
    5. (2005). FunCat 105 functional assignment by Belief Propagation.
    6. (2002). How well do we understand the clusters found in microarray data?
    7. (2006). MIPS: analysis and annotation of proteins from whole genomes in 2005.
    8. Mu ¨nsterko ¨tter,M. et al. (2004) 80 The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.
    9. (2004). Network motifs in integrated cellular networks of transcription-regulation and protein–protein interaction.
    10. (2003). Spurious spatial periodicity of co-expression in microarray data due to printing 85 design.
    11. (1999). Systematic determination of genetic network architecture. 90

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