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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 publications:
  • Hooper CM, Tanz SK, Castleden I, Vacher M, Small I; Millar, AH (2014) SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome. Bioinformatics. 30(23): 3356-64 (Bioinformatics.) (PubMed)

  • 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)

Contact

Harvey Millar (harvey.millar(at)uwa.edu.au)
Cornelia Hooper (cornelia.hooper(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.

SUBA4

suba logo

There is a newer version of SUBA that is being updated with the latest experimental evidence:

http://suba.live

It was published in January 2017. SUBA3 (below) is no longer being updated.

SUBA3 News

  • Looking for crop protein localisations? !!!NEW!!! subcellular localisation resource for wheat, barley, rice and maize has 8 predictions and experimental data up to mid 2014: access cropPAL

  • Most recent publications: SUBAcon (Bioinformatics) (PubMed) and SUBA3 (Nucleic Acids Res.) (PubMed).
  • For security reasons SUBA2 has been removed. Suba2 will now redirect to SUBA3.
  • Last updates: Bibliographic references: 18.01.2016 and SUBAcon training: 31.06.2014
  • Data in SUBA3: GFP & MS localisation data, Protein-protein interaction, 22 Pre-computed localisation predictions, TAIR10 annotations

New Data

  • To submit your subcellular location data please follow this link: . We will assess your data and then deposit it in the SUBA3 database.
  • Alternatively, you can send an email directly to Cornelia Hooper (cornelia.hooper [at] uwa.edu.au) or Sandra Tanz (sandra.tanz [at] uwa.edu.au)

Quick Search

submit Query

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)