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LOCATE: a mouse protein subcellular localization database.

J Lynn Fink1, Rajith N Aturaliya, Melissa J Davis

  • 1ARC Centre in Bioinformatics, University of Queensland, St Lucia, Queensland 4072, Australia. l.fink@imb.uq.edu.au

Nucleic Acids Research
|December 31, 2005
PubMed
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We created LOCATE, a database detailing protein membrane organization and subcellular localization for the mouse proteome. This resource consolidates high-throughput computational and experimental data for enhanced biological discovery.

Area of Science:

  • Proteomics
  • Cell Biology
  • Bioinformatics

Background:

  • Understanding protein localization is crucial for deciphering cellular functions and disease mechanisms.
  • Existing resources for protein localization data are fragmented and often lack high-throughput experimental validation.
  • The FANTOM3 Isoform Protein Sequence set provides a comprehensive collection of mammalian protein sequences.

Purpose of the Study:

  • To develop LOCATE, a centralized, web-accessible database for protein membrane organization and subcellular localization data.
  • To catalogue experimentally verified localization and membrane organization for a significant portion of the mouse proteome.
  • To integrate data from high-throughput computational and experimental methods.

Main Methods:

  • Membrane organization predicted using the high-throughput computational pipeline MemO.

Related Experiment Videos

  • Subcellular localization determined via high-throughput immunofluorescence assays.
  • Manual curation of localization data from over 1700 peer-reviewed publications.

    • Main Results:

    • LOCATE provides curated data on membrane organization and subcellular localization for mammalian proteins.
    • The database includes localization data for approximately 40% of the mouse proteome.
    • This represents the first high-throughput effort to catalogue experimentally verified subcellular locations and membrane organization.

    Conclusions:

    • LOCATE serves as a valuable, publicly accessible resource for researchers studying protein localization and membrane organization.
    • The database facilitates a deeper understanding of mammalian cell biology and protein function.
    • High-throughput approaches are effective for generating comprehensive protein localization datasets.