CORUM: the Comprehensive Resource of Mammalian Protein Complexes

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2007 Oct 30

PMID 17965090

Citations 195

Authors

Andreas Ruepp

Barbara Brauner

Irmtraud Dunger-Kaltenbach

Goar Frishman

Corinna Montrone

Michael Stransky

Brigitte Waegele

Thorsten Schmidt

Octave Noubibou Doudieu

Volker Stumpflen

H Werner Mewes

Affiliations

Soon will be listed here.

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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References

Kim P, Lu L, Xia Y, Gerstein M . Relating three-dimensional structures to protein networks provides evolutionary insights. Science. 2006; 314(5807):1938-41. DOI: 10.1126/science.1136174. View

Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M . The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004; 32(18):5539-45. PMC: 524302. DOI: 10.1093/nar/gkh894. View

Yu H, Luscombe N, Lu H, Zhu X, Xia Y, Han J . Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 2004; 14(6):1107-18. PMC: 419789. DOI: 10.1101/gr.1774904. View

Fraser H . Modularity and evolutionary constraint on proteins. Nat Genet. 2005; 37(4):351-2. DOI: 10.1038/ng1530. View

Luc P, Tempst P . PINdb: a database of nuclear protein complexes from human and yeast. Bioinformatics. 2004; 20(9):1413-5. DOI: 10.1093/bioinformatics/bth114. View

Bader G, Betel D, Hogue C . BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 2003; 31(1):248-50. PMC: 165503. DOI: 10.1093/nar/gkg056. View

. The Universal Protein Resource (UniProt). Nucleic Acids Res. 2006; 35(Database issue):D193-7. PMC: 1669721. DOI: 10.1093/nar/gkl929. View

Krogan N, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A . Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006; 440(7084):637-43. DOI: 10.1038/nature04670. View

Jensen L, Jensen T, de Lichtenberg U, Brunak S, Bork P . Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature. 2006; 443(7111):594-7. DOI: 10.1038/nature05186. View

10.

Gavin A, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M . Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006; 440(7084):631-6. DOI: 10.1038/nature04532. View

11.

Hart G, Lee I, Marcotte E . A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics. 2007; 8:236. PMC: 1940025. DOI: 10.1186/1471-2105-8-236. View

12.

Pereira-Leal J, Levy E, Teichmann S . The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci. 2006; 361(1467):507-17. PMC: 1609335. DOI: 10.1098/rstb.2005.1807. View

13.

Mishra G, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P . Human protein reference database--2006 update. Nucleic Acids Res. 2005; 34(Database issue):D411-4. PMC: 1347503. DOI: 10.1093/nar/gkj141. View

14.

Alberts B . The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell. 1998; 92(3):291-4. DOI: 10.1016/s0092-8674(00)80922-8. View

15.

Mewes H, Frishman D, Mayer K, Munsterkotter M, Noubibou O, Pagel P . MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 2005; 34(Database issue):D169-72. PMC: 1347510. DOI: 10.1093/nar/gkj148. View

16.

Birney E, Stamatoyannopoulos J, Dutta A, Guigo R, Gingeras T, Margulies E . Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007; 447(7146):799-816. PMC: 2212820. DOI: 10.1038/nature05874. View

17.

Ruepp A, Doudieu O, van den Oever J, Brauner B, Dunger-Kaltenbach I, Fobo G . The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res. 2005; 34(Database issue):D568-71. PMC: 1347437. DOI: 10.1093/nar/gkj074. View

18.

Guldener U, Munsterkotter M, Kastenmuller G, Strack N, van Helden J, Lemer C . CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res. 2004; 33(Database issue):D364-8. PMC: 540007. DOI: 10.1093/nar/gki053. View

19.

Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes H . MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2005; 34(Database issue):D436-41. PMC: 1347366. DOI: 10.1093/nar/gkj003. View

20.

Lage K, Karlberg E, Storling Z, Olason P, Pedersen A, Rigina O . A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol. 2007; 25(3):309-16. DOI: 10.1038/nbt1295. View