institute of bioinformatics and systems biology / mips

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Genome Annotation

With the completion of the genome sequence of Saccharomyces cerevisiae (1) MIPS was established as a research centre for manual annotation of complete genomes. Since then genomes from all domains of life have been manually annotated (see below). Functional information from experimentally investigated proteins are obtained by the evaluation of scientific articles. For proteins that have neither been manually annotated nor experimentally characterized, a semi-automatic functional annotation using gSPC clustering (10) and heterogeneous relational Markov networks is provided.

Functional Classification

For the assignment of functional information to proteins, we are using the Functional Catalogue (FunCat) annotation scheme (7).

Annotation of Functional Units

Biological processes are controlled by the interaction of molecules which form complex functional networks (functional modules). Therefore, the investigation of biomolecular networks takes centre stage in systems biology these days. We address the analysis of functional modules in mammals at three levels: protein-protein interactions, protein complexes and functional modules. Currently, we provide two resources: The Mammalian Protein-Protein Interaction database MPPI (5,8) and the mammalian protein complex database CORUM (12). Our mid-term goal is to establish a reference dataset of manually annotated functional modules.

Manually annotated Genomes

  • Archaea
    • Thermoplasma acidophilum (2)
  • Bacteria
    • Listeria monocytogenes EGD (9,10)
    • Listeria innocua Clip11262 (9,10)
    • Helicobacter pylori KE26695 (ATCC 700392) (9,10)
    • Bacillus subtilis (9,10)
    • Desulfotalea psychrophila (6)
  • Fungi
    • Saccharomyces cerevisiae (1)
    • Neurospora crassa (3,4)
  • Mammalia

Staff

Andreas Ruepp andreas.ruepp@helmholtz-muenchen.de
Barbara Brauner
Irmtraut Dunger-Kaltenbach
Gisela Fobo
Goar Frishman
Corinna Montrone

Reference List

  1. Mewes, H.W. et al. (1997) Overview of the yeast genome. Nature, 387, 7-8.
  2. Ruepp, A. et al. (2000) The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature, 407, 508-513.
  3. Galagan, J.E. et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422, 859-868.
  4. Mannhaupt, G. et al. (2003) What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence. Nucl.Acids.Res., 31, 1944-1954.
  5. Mewes, H.W. et al. (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res., 32, D41-D44.
  6. Rabus, R. et al. (2004) The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol.,6, 887-902.
  7. Ruepp, A. et al. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucl.Acids.Res., 32, 5539-45
  8. Pagel, P. et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-4.
  9. Tetko, I.V. et al. (2005) MIPS bacterial genomes functional annotation benchmark dataset. Bioinformatics, 21, 2520-1.
  10. Tetko, I.V. et al. (2005) Super paramagnetic clustering of protein sequences. BMC Bioinformatics, 6, 82.
  11. Artamonova, I.I. et al. (2005) Mining sequence annotation databanks for association patterns. Bioinformatics, 21, iii49-iii57.
  12. Ruepp, A. et al. (2007) CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res., Advance Access.
  13. Güldener, U. et al. (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res., 34, D436-41.
  14. Ruepp, A. et al. (2006) The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res., 34, D568-71.
  15. Prokisch, H. et al. (2006) MitoP2: the mitochondrial proteome database--now including mouse data. Nucleic Acids Res., 34, D705-11.
  16. Lehner, A. et al.(2006) Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism. Syst Appl Microbiol.