Welcome to SUBA4

What is SUBA?

SUBA is the central resource for Arabidopsis protein subcellular location data. Proteins have specific functions and locations within the plant cell. They generate or are themselves products important for plant growth and response. Protein subcellular location and the proximity relationship of proteins are important clues to function within the metabolic household. Subcellular location can be determined by fluorescent protein tagging or mass spectrometry detection in subcellular purifications and by prediction using protein sequence features.

SUBA provides a subcellular data query platform, protein sequence BLAST alignment, a high confidence subcellular locations reference standards and analytic tools.
Find out all about SUBA4
Find the SUBA4 Tutorial Page
Cite SUBA using the citation guide

SUBA citation guide

Data Citation

If you find our SUBA resources useful please help us grow and cite us.

What is data citation? When using data generated by an author, it is the practice of providing a reference to the data source or description. This is important because increased citations of data sets imply significance and validity, it enables the authos to get recognized for their efforts. Overall the use of data, intellectual property and other resources should be appropriately attributed when published on downstream outputs. For more informations on citing data please visit this resource.

Since SUBA is a mixed resource derived from collated data sets and generated data, it is not always clear how to cite this. All data sets retrieved from other published studies have been directly linked to their repository record in PUBMED. This is how we directly acknowledge every localisation or Protein-Protein interaction we collate into SUBA. If you query SUBA and retrieve a mixed data set from a number of studies it is more applicable to cite the latest SUBA publication as the method to retrieve the data as one reference.
When using SUBA bulk data downloads, please also cite Research Data Online at the University of Western Australia including the Digital Object Identifier (DOI). The SUBA collection archive can be accessed using the DOI: 10.4225/23/581055ddcb1ce.

Citing SUBA

If you have used the SUBA search interphase for refining, retrieving and interpreting your data please cite SUBA4:
Hooper CM, Castleden I, Tanz SK, Aryamanesh, and Millar, AH (2017) SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations Nucleic Acids Res. Jan 4;45(D1):D1064-D1074. doi: 10.1093/nar/gkw1041 (PubMed)

If you perfom large-scale data analysis using predominantly SUBAcon calls please cite also our study explaining the algorithm SUBAcon in your methods:
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. (PubMed)

SUBA publication history

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 (PubMed)

Heazlewood JL1, Verboom RE, Tonti-Filippini J, Small I, Millar AH (2007) SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res. 35:D213-8. (PubMed)

Heazlewood JL1, 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)

SUBA dataset in repositories available for bulk downloads in sql and csv format

The SUBA4 full data download is archived in Research Data Online. If you used data sets from the download in your study please cite SUBA this way:
Hooper CM, Castleden I, Tanz SK, Aryamanesh, and Millar, AH (2017). SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. doi:10.4225/23/581055ddcb1ce

The SUBA3 full data download is archived in Research Data Online.

SUBA4 Notice board

!!Coming Soon: We are updating SUBA to include experimental localisation up to 2020.

A description of SUBA4 is now available at Nucleic Acids Res.
Looking for crop protein localisations? Find them at cropPAL for wheat, barley, rice and maize.

NEW data in SUBA4

More localisations and experimental suborganellar localisations and protein-protein interaction localisations
The SUBA4 toolbox for estimating organellar protein abundance (MMAP tool) and protein-protein location relationships (CAT and PAT)

Updates

Bibliographic references were last updated: 30th June 2017.
SUBAcon was last retrained using data up to: 30th June 2017.

Can't find what you are looking for? Email directly to Cornelia Hooper (cornelia.hooper [at] uwa.edu.au)

Try out an instant query for AT2G33210.1

Quick Search

The quick search will search for AGIs in your input as well as search the TAIR descriptions and abstracts of experimental studies for any matching keywords that you provided.

Find the closest Arabidopsis BLAST match to your sequence

... below protein sequence fragments have BLAST similarity bit-scores ↓

Bit Score is log₂N_eff-log₂(E-value) where E-value = p_val × N_eff is the p-value times the effective search space size. The larger the bit-score the better since p_val = P(random seq having a better score) = 2^-(bit-score). The p-value measures the statistical significance of the match but since we tried N_eff times to find a match we need to make a correction. Multiplying by the number of possible matches gives the e-value or the expected number of hits with a better match just by random chance. (See here).

SUBA4 help menu

How to search SUBA4?

A step-by-step tutorial explaining how to use SUBA4 is available at: SUBA4 tutorials.

How to submit new subcellular localization data to SUBA4?

SUBA is updated annually with the latest update date shown on the home page notice board. If you have published or found data that is not in SUBA please submit this subcellular location data to us. Currently we accept data in the format of PubMedID;location;AGI (e.g. 25900983;golgi;AT5G16280.1). The location categories must be cytoskeleton, cytosol, endoplasmic reticulum, extracellular, golgi, mitochondrion, nucleus, peroxisome, plasma membrane, plastid or vacuole. If you have data fitting these criteria please follow this link:

We will assess your data and add it to our next scheduled update. If you have suborganellar data for any other location categories or Protein-Protein interaction data, please contact:

Cornelia Hooper (cornelia.hooper(at)uwa.edu.au)

Can't get the right data out SUBA4?

If you have specific questions that you cannot pose through the SUBA4 interface, we may be able to help you. We can source, link and combined more types of data than the window to SUBA4 shows. We are open to collaborations and involvement with our users. If you encounter any problems with the SUBA4 interface or find any errors with the data in SUBA4, please contact us:

Cornelia Hooper (cornelia.hooper(at)uwa.edu.au)
Ian Castleden (ian.castleden(at)uwa.edu.au)
Harvey Millar (harvey.millar(at)uwa.edu.au)