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CORUM: the comprehensive resource of mammalian protein complexes.

Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stümpflen V, Mewes HW - Nucleic Acids Res. (2007)

Bottom Line: A web-based system is available to query, view and download the data.CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases.Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes.

View Article: PubMed Central - PubMed

Affiliation: Institute for Bioinformatics (MIPS), German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany. andreas.ruepp@gsf.de

ABSTRACT
Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes.

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Overview about the FunCat functional annotation results of the protein complexes in CORUM. The different search options of the database are also shown.
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Figure 1: Overview about the FunCat functional annotation results of the protein complexes in CORUM. The different search options of the database are also shown.

Mentions: We use the Functional Catalogue (FunCat) annotation scheme for protein and protein complex function characterization (14). The FunCat has been used for manual annotation of model organisms like Saccharomyces cerevisiae, Arabidopsis thaliana and mouse (15) and was also frequently used for the analysis of protein networks and high-throughput experiments (14). Application of FunCat organizes data in a systematic, computer-readable format. The hierarchical structure of FunCat allows browsing for protein complexes with particular cellular functions or localizations (Figure 1). This reveals subsets, which would otherwise require specialised databases like the PIN database for nuclear protein complexes (16). Examples of such sub datasets are presented on the CORUM home page. In addition, FunCat annotation allows fast access to some statistics of the data. The CORUM dataset contains e.g. far more protein complexes from the nucleus (67% of all complexes with annotated localization) than from the cytoplasm (9%). This might be explained by the complexity of the information processes within the nucleus. However, the data do not necessarily correlate to the situation of living cells but might rather reflect the topics which have been investigated by individual research projects.Figure 1.


CORUM: the comprehensive resource of mammalian protein complexes.

Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stümpflen V, Mewes HW - Nucleic Acids Res. (2007)

Overview about the FunCat functional annotation results of the protein complexes in CORUM. The different search options of the database are also shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238909&req=5

Figure 1: Overview about the FunCat functional annotation results of the protein complexes in CORUM. The different search options of the database are also shown.
Mentions: We use the Functional Catalogue (FunCat) annotation scheme for protein and protein complex function characterization (14). The FunCat has been used for manual annotation of model organisms like Saccharomyces cerevisiae, Arabidopsis thaliana and mouse (15) and was also frequently used for the analysis of protein networks and high-throughput experiments (14). Application of FunCat organizes data in a systematic, computer-readable format. The hierarchical structure of FunCat allows browsing for protein complexes with particular cellular functions or localizations (Figure 1). This reveals subsets, which would otherwise require specialised databases like the PIN database for nuclear protein complexes (16). Examples of such sub datasets are presented on the CORUM home page. In addition, FunCat annotation allows fast access to some statistics of the data. The CORUM dataset contains e.g. far more protein complexes from the nucleus (67% of all complexes with annotated localization) than from the cytoplasm (9%). This might be explained by the complexity of the information processes within the nucleus. However, the data do not necessarily correlate to the situation of living cells but might rather reflect the topics which have been investigated by individual research projects.Figure 1.

Bottom Line: A web-based system is available to query, view and download the data.CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases.Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes.

View Article: PubMed Central - PubMed

Affiliation: Institute for Bioinformatics (MIPS), German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany. andreas.ruepp@gsf.de

ABSTRACT
Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes.

Show MeSH
Related in: MedlinePlus