SUBA version 2.21

SUB-cellular location database for Arabidopsis proteins (SUBA)

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.

Dr Joshua Heazlewood

SUBA paper recognised by ISI as triggering a fast-moving research front

The SUBA database, established and maintained by the Centre tracks new data on the subcellular location of proteins in the model plant Arabidopsis. This is rapidly becoming the central reference point for researchers on the issue of where a protein resides in plant cells. Just this month Thomson ISI recognised the high citation rate of the original SUBA paper by selecting it in ISI's Fast Moving Fronts for November. An interview with the first author, former PEB researcher Dr Joshua Heazlewood, is now on the ISI website, or you could download the PDF.

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 SUBA. The database has a web accessible interface that allows advanced combinatorial queries to be undertaken on the contained data.

Search SUBA

A PDF tutorial explaining how to use SUBA is available here: SUBA tutorial.

SUBA houses large scale proteomic and GFP localisation sets from cellular compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular localisations. SUBA was last updated in June 2009 and is based on the TAIR8 genome annotation release.

SUBA query construction:

Select the 'SEARCH' tab.
The phrase 'Search for Arabidopsis proteins where...', displayed at the top, represents the beginning of the Boolean sentence that will form your query.
Each row of pull down menus work in combination to construct a query and each combination can be added to the main query pane by pushing the 'Add' button at the end of the row.

Easy query

The first row of pull down menus provides access to the majority of experimental localisation data. Using the 3 pull down menus, a query can be built to investigate, for example, plastid localised proteins by mass spectrometry. To access such a set of proteins:

Leave the first pull down menu (Experimentally observed location) as 'is'.
In the second menu (inferred by) select the option 'MS/MS assay'.
The third pull down menu (to be in) contains the subcellular location tags, select 'plastid'.
Activate your query combination using the 'Add' button at the end of the row.
The built query sentence will appear in the top window under 'Search for Arabidopsis proteins where...' with the statement 'Protein location is inferred by MS/MS assay to be in plastid'.
Query the database by pushing the 'Submit' button at the bottom of the page.

More complex query

Select the Boolean linkers 'AND' or 'OR' command buttons to built more complex queries.

To search for plastid proteins identified through mass spectrometry and GFP analysis:

Extend the initial query sentence from above by selecting the Boolean linker 'AND'. The 'Add' buttons at the end of each row become activated again.
Leave the first pull down menu (Experimentally observed location) as 'is'.
In the second menu (inferred by) select the option 'GFP assay'.
The third pull down menu (to be in) contains the subcellular location tags, select 'plastid'.
The built query sentence will appear in the top window under 'Search for Arabidopsis proteins where...' with the statement 'Protein location is inferred by MS/MS assay to be in plastid' AND 'Protein location is inferred by GFP assay to be in plastid'.
Query the database by pushing the 'Submit' button at the bottom of the page.

Use the linker buttons 'AND' or 'OR' to include:

Pre-computed predictions of localisation for 10 prediction programs for all ~30,000 Arabidopsis proteins. Access data through the 'Predicted location (is/is not) predicted by (predictor) to be in (location)' menu row.
Subcellular claims by different research papers using the 'Literature referenced location (is/is not) described in (paper)' menu row
Text based searches of descriptor fields through the 'Protein description (contains/does not contain) keyword (e.g. protein kinase)' menu row.
Physio-chemical parameters such as molecular weight, EST number, chromosomal location. Use the 'Physical properties' and 'Underlying gene model (is on/is not on) chromosome (number)' menu rows.
A user defined protein set by using a list of AGI identifiers through the 'Arabidopsis Gene Identifier (is in list/is not in list)' menu row. Enter the AGI numbers in the box below.

Use the 'Undo' button to remove any mistakes from the forming query. This removes the last entered query.

Use the 'Clear' button to remove the entire constructed query.

Use the 'Submit' button to query the database.

SUBA Results

Once a query has been submitted the contents of the 'RESULT' tab will automatically be displayed. By default 8 columns will be displayed: AGI, TAIR descriptor, location summaries of all predictors, location by Mass Spec, location by GFP, location by annotation (TAIR), location by AmiGO and location by UniProt.

Results can be sorted by field using the function menu. The function menu is activated by tracking the mouse over the column header and then selecting the emerging arrow. New columns can be added to the Result tab window by selecting 'Columns' in the function menu.

Columns can be organized using mouse drag and drop functionality.

Only 50 rows of data are displayed with further rows available using the 'Next Page' or 'Last Page' buttons at the bottom left of the Result tab window.

The codes or unique identifiers (uid) beside each location are links to the primary data source for each entry at PubMed or ISI.

Each AGI provides a link to a summary page (SUBA Flatfile) for the entry. The flatfile contains a detailed breakdown of subcellular localisation information (experimental and predicted), description and sequence information (TAIR8), physio-chemical characteristics, a hydropathy plot, and links to the same entry at other Arabidopsis databases.

All results can be downloaded as a tab delimited file by using the 'Download All Results' button at the top left of the Result tab window. By default this file opens in Excel.

For detailed description on how to use SUBA refer to the SUBA tutorial.

SUBA Statistics

Current subcellular location data available in SUBA:

2232 entries based on chimeric fusion studies, comprising 1450 distinct proteins from 738 publications.
9603 entries based on subcellular proteomic studies, comprising 4603 distinct proteins from 64 publications.

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Citing SUBA

If you find this resource useful please cite one of the following two publications:

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 (hmillar(at)cyllene.uwa.edu.au) or Julian Tonti-Filippini (tontis(at)iinet.net.au) or Sandra Tanz (stanz(at)cyllene.uwa.edu.au)