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What is SUBA?

SUBA provides a powerful tool to investigate subcellular localisation in Arabidopsis through the unification of disparate datasets and through the provision of a web accessible interface for the construction of powerful user based queries resulting in a one-stop-shop for protein localisation in this model plant.

SUBA3 houses large scale proteomic and GFP localisation sets from cellular compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular localisations. Protein-protein interaction data allow the search for interacting protein pairs.

Why SUBA?

Subcellular localisation information can contribute towards our understanding of protein function, protein redundancy and of biological inter-relationships. While a variety of technologies are currently employed to determine the sub-cellular location of proteins, much of this information is not available in an integrated manner. In an attempt to get a clearer picture of our experimental data and to more generally understand subcellular partitioning we have brought together various data sources to build SUBA3. The database has a web accessible interface that allows advanced combinatorial queries to be undertaken on the contained data.



Citing SUBA

If you find this resource useful please cite one of the following three publications:
  • Tanz SK, Castleden I, Hooper CM, Vacher M, Small I; Millar, AH (2013) SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res. 41: D1185-91 (Nucleic Acids Res.) (PubMed)
  • Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I and Millar AH. (2007) SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res. 35: D213-D218. (PubMed)
  • Heazlewood JL, Tonti-Filippini J, Verboom RE, Millar AH. (2005) Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. Plant Physiol. 139(2): 598-609. (PubMed)

Contact

Harvey Millar (harvey.millar(at)uwa.edu.au)
Ian Castleden (ian.castleden(at)uwa.edu.au)
Sandra Tanz (sandra.tanz(at)uwa.edu.au)



Search Example:

Welcome to SUBA3

The SUBcellular localisation database for Arabidopsis proteins.

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Send us your subcellular localization data

How to submit your data

  • We require the data in the form:
    "PubMedID{sep}Location{sep}AGI" where {sep} is a comma or a tab or a space.
  • One AGI per line.
  • Location must be one that SUBA3 recognises: cytoskeleton, cytosol, endoplasmic reticulum, extracellular, golgi, mitochondrion, nucleus, peroxisome, plasma membrane, plastid or vacuole.
  • AGIs that are not in TAIR10 will be ignored.
  • Duplicates will be ignored: that means we have already added your data to SUBA.
  • AGIs without splice isoforms will automatically have the .1 added.
  • PubMed IDs are 5-12 digits
PubMedID{sep}Location{sep}AGI
OR: 
Any problems contact:
Sandra Tanz
(sandra.tanz [at] uwa.edu.au),
Cornelia Hooper
(cornelia.hooper [at] uwa.edu.au) or
Ian Castleden
(ian.castleden [at] uwa.edu.au)