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LOCATE: a mammalian protein subcellular localization database.

Josefine Sprenger1, J Lynn Fink, Seetha Karunaratne

  • 1ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.

Nucleic Acids Research
|November 8, 2007
PubMed
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The LOCATE database now offers extensive protein localization data for mouse and human proteomes, including computational predictions and image analysis. This resource aids systematic investigations into subcellular compartments.

Area of Science:

  • Proteomics
  • Cell Biology
  • Bioinformatics

Background:

  • Accurate protein subcellular localization is crucial for understanding cellular function and disease.
  • Existing databases may lack comprehensive, curated data on protein localization across different species.
  • The RIKEN FANTOM Consortium provides extensive protein isoform sequence sets for mouse and human.

Purpose of the Study:

  • To enhance and expand the LOCATE database with updated protein localization information.
  • To provide a comprehensive, web-accessible resource for mouse and human protein localization data.
  • To integrate diverse data types, including experimental, computational, and literature-derived information.

Main Methods:

  • Curating and integrating high-quality experimental protein localization data.

Related Experiment Videos

  • Incorporating computational predictions for subcellular localization.
  • Developing automated methods for classifying experimental localization image data.
  • Adding protein sorting signal predictions and third-party literature data submissions.

    • Main Results:

    • LOCATE now contains high-quality localization data for 20% of the mouse proteome.
    • General localization annotation covers nearly 36% of the mouse proteome.
    • The database annotates 58,128 mouse and 64,637 human protein isoforms.
    • Includes computational predictions and automated image data classification.

    Conclusions:

    • The expanded LOCATE database offers a valuable resource for studying protein organization within subcellular compartments.
    • This comprehensive proteome localization data will support future systematic biological investigations.
    • LOCATE serves as a key platform for researchers investigating protein function and cellular architecture.