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. 2007 Jan;35(Database issue):D213-8.
doi: 10.1093/nar/gkl863. Epub 2006 Oct 28.

SUBA: the Arabidopsis Subcellular Database

Joshua L Heazlewood  1 , Robert E Verboom, Julian Tonti-Filippini, Ian Small, A Harvey Millar
Affiliations

SUBA: the Arabidopsis Subcellular Database

Joshua L Heazlewood et al. Nucleic Acids Res. 2007 Jan.

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 approximately 2600 proteins. Further protein localisation information may be obtained from other literature references to analysis of locations (AmiGO: approximately 900 proteins), location information from Swiss-Prot annotations (approximately 2000 proteins); and location inferred from gene descriptions (approximately 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).

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Figures

Figure 1
Figure 1
The SUBA graphical user interface showing a search (A) where complex queriescan be built from pull down menus and visualised in the sentence structure represented in the text box. In this case for proteins localised to mitochondria by three different experimental data sets. The results (B) of this search is shown, and the AGI page (C) for one of these identifications giving links and information on the requested protein.
See this image and copyright information in PMC

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