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Related Experiment Videos

SUBA: the Arabidopsis Subcellular Database.

Joshua L Heazlewood1, Robert E Verboom, Julian Tonti-Filippini

  • 1ARC Centre of Excellence in Plant Energy Biology, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia 35 Stirling Highway, Crawley 6009, Western Australia, Australia. botjlh@cyllene.uwa.edu.au

Nucleic Acids Research
|October 31, 2006
PubMed
Summary
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The SUBA database integrates diverse protein localization data for Arabidopsis, aiding research into protein function and biological relationships. This resource compiles information from multiple experimental and computational methods for over 6743 non-redundant proteins.

Area of Science:

  • Plant biology
  • Proteomics
  • Bioinformatics

Background:

  • Understanding protein localization is crucial for deciphering protein function and biological interactions.
  • Existing methods for determining protein localization, including fluorescent fusion proteins and mass spectrometry, generate vast datasets.
  • Integrating these diverse data sources is essential for a comprehensive view of subcellular organization.

Purpose of the Study:

  • To develop SUBA, a centralized database for Arabidopsis protein subcellular localization.
  • To consolidate protein localization data from various experimental and computational sources into a single, accessible resource.
  • To facilitate the study of protein function and biological inter-relationships in Arabidopsis.

Main Methods:

  • Compilation of data from fluorescent fusion protein experiments (approx. 1100 experiments).

Related Experiment Videos

  • Integration of mass spectrometry-based proteomic surveys (approx. 2600 proteins).
  • Inclusion of data from literature (AmiGO), Swiss-Prot annotations, gene descriptions, and computational predictions.

    • Main Results:

    • The SUBA database contains localization data for over 6743 non-redundant Arabidopsis proteins.
    • Data encompasses 10 distinct subcellular locations.
    • The database represents proteins encoded by transcripts responsible for 51% of Arabidopsis expressed sequence tags.

    Conclusions:

    • SUBA provides a powerful, integrated resource for assessing protein subcellular localization in Arabidopsis.
    • The database enhances our understanding of Arabidopsis proteome organization and protein function.
    • SUBA serves as a valuable tool for plant biologists and researchers in related fields.