SUBA: the Arabidopsis subcellular database

J.L. Heazlewood, Robert Verboom, Julian Tonti-Filippini, Ian Small, Harvey Millar

Research output: Contribution to journalArticle

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Abstract

Knowledge of protein localisation contributes towards our understanding of protein function and of biological inter-relationships. A variety of experimental methods are currently being used to produce localisation data that need to be made accessible in an integrated manner. Chimeric fluorescent fusion proteins have been used to define subcellular localisations with at least 1100 related experiments completed in Arabidopsis. More recently, many studies have employed mass spectrometry to undertake proteomic surveys of subcellular components in Arabidopsis yielding localisation information for similar to 2600 proteins. Further protein localisation information may be obtained from other literature references to analysis of locations (AmiGO: similar to 900 proteins), location information from Swiss-Prot annotations (similar to 2000 proteins); and location inferred from gene descriptions (similar to 2700 proteins). Additionally, an increasing volume of available software provides location prediction information for proteins based on amino acid sequence. We have undertaken to bring these various data sources together to build SUBA, a SUBcellular location database for Arabidopsis proteins. The localisation data in SUBA encompasses 10 distinct subcellular locations, > 6743 non-redundant proteins and represents the proteins encoded in the transcripts responsible for 51% of Arabidopsis expressed sequence tags. The SUBA database provides a powerful means by which to assess protein subcellular localisation in Arabidopsis (http://www.suba.bcs.uwa.edu.au).
LanguageEnglish
PagesD213-D218
JournalNucleic Acids Research
Volume35
Issue numberSupp. 1
DOIs
StatePublished - 2007

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Arabidopsis
Databases
Proteins
Arabidopsis Proteins
Information Storage and Retrieval
Expressed Sequence Tags
Proteomics
Amino Acid Sequence
Mass Spectrometry
Software

Cite this

Heazlewood, J.L. ; Verboom, Robert ; Tonti-Filippini, Julian ; Small, Ian ; Millar, Harvey. / SUBA: the Arabidopsis subcellular database. In: Nucleic Acids Research. 2007 ; Vol. 35, No. Supp. 1. pp. D213-D218
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SUBA: the Arabidopsis subcellular database. / Heazlewood, J.L.; Verboom, Robert; Tonti-Filippini, Julian; Small, Ian; Millar, Harvey.

In: Nucleic Acids Research, Vol. 35, No. Supp. 1, 2007, p. D213-D218.

Research output: Contribution to journalArticle

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