Data

SUB-cellular location database for Arabidopsis proteins

Also known as: SUBA, SUBA2, SUBA3
The University of Western Australia
Dr Cornelia Hooper (Managed by) Dr Ian Castleden (Managed by) Professor Ian Small (Managed by, Aggregated by) Winthrop Professor Harvey Millar (Aggregated by) Winthrop Professor Jim Whelan (Aggregated by)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=http://suba.plantenergy.uwa.edu.au/&rft.title=SUB-cellular location database for Arabidopsis proteins&rft.identifier=http://suba.plantenergy.uwa.edu.au/&rft.publisher=The University of Western Australia&rft.description=The SUB-cellular location database for Arabidopsis proteins (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. 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 their experimental data and to more generally understand subcellular partitioning we have brought together various data sources to build SUBA. The database has a web accessible interface that allows advanced combinatorial queries to be undertaken on the contained data. SUBA houses large scale proteomic data sets and GFP localisation from cellular compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular localisations. With the upgrade to SUBA3, protein-protein-interaction data was added and more recently a classification algorithm SUBAcon was integrated for forming a localisation consensus call. SUBA was last updated in June 2014 and is based on the TAIR10 genome annotation release. The experimental data sets are generally updated annually mid year. SUBA3 in January 2015 contains 4725 entries based on chimeric fusion studies (GFP), comprising 2987 distinct proteins from 1414 publications as well as 27601 entries based on subcellular proteomic studies, comprising 8787 distinct proteins from 143 publications. There are 27385 protein-protein-interaction pairs stored in SUBA3.&rft.creator=Australian Research Council Centre of Excellence in Plant Energy Biology&rft.creator=Professor Ian Small&rft.creator=Winthrop Professor Harvey Millar&rft.creator=Winthrop Professor Jim Whelan&rft.creator=Winthrop Professor Steven Smith&rft.date=2014&rft.relation=10.3389/fpls.2014.00396 &rft.relation= 10.1093/bioinformatics/btu550&rft.relation=10.1093/nar/gks1151&rft_subject=Plant Cell and Molecular Biology&rft_subject=BIOLOGICAL SCIENCES&rft_subject=PLANT BIOLOGY&rft.type=dataset&rft.language=English Access the data
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The database is freely accessible from the url: http://suba.plantenergy.uwa.edu.au/ For further access rights to datasets please contact plantenergy@uwa.edu.au.


Contact Information

Postal Address:
School of Biomedical, Biomolecular and Chemical Sciences The University of Western Australia35 Stirling HighwayCrawley, PerthWestern Australia 6009
Ph: (+61 8) 6488 4414
Fax: (+61 8) 6488 7330

Street Address:
Bayliss Building, Fairway entrance number 4, Crawley campus



Full description

The SUB-cellular location database for Arabidopsis proteins (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. 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 their experimental data and to more generally understand subcellular partitioning we have brought together various data sources to build SUBA. The database has a web accessible interface that allows advanced combinatorial queries to be undertaken on the contained data.

SUBA houses large scale proteomic data sets and GFP localisation from cellular compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular localisations. With the upgrade to SUBA3, protein-protein-interaction data was added and more recently a classification algorithm SUBAcon was integrated for forming a localisation consensus call. SUBA was last updated in June 2014 and is based on the TAIR10 genome annotation release. The experimental data sets are generally updated annually mid year.


SUBA3 in January 2015 contains 4725 entries based on chimeric fusion studies (GFP), comprising 2987 distinct proteins from 1414 publications as well as 27601 entries based on subcellular proteomic studies, comprising 8787 distinct proteins from 143 publications. There are 27385 protein-protein-interaction pairs stored in SUBA3.

Data time period: 07 2009

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Biological Sciences | Plant Biology | Plant Cell and Molecular Biology |

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