SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis

Sandra K Tanz, Ian Castleden, Cornelia M Hooper, Michael Vacher, Ian Small, A Harvey Millar

Research output: Contribution to journalArticle

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Abstract

The subcellular location database for Arabidopsis proteins (SUBA3, http://suba.plantenergy.uwa.edu.au) combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization and protein-protein interaction (PPI) datasets with subcellular targeting calls from 22 prediction programs. More than 14 500 new experimental locations have been added since its first release in 2007. Overall, nearly 650 000 new calls of subcellular location for 35 388 non-redundant Arabidopsis proteins are included (almost six times the information in the previous SUBA version). A re-designed interface makes the SUBA3 site more intuitive and easier to use than earlier versions and provides powerful options to search for PPIs within the context of cell compartmentation. SUBA3 also includes detailed localization information for reference organelle datasets and incorporates green fluorescent protein (GFP) images for many proteins. To determine as objectively as possible where a particular protein is located, we have developed SUBAcon, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein's location in the cell. The probabilities of subcellular location for each protein are provided and displayed as a pictographic heat map of a plant cell in SUBA3.
LanguageEnglish
PagesD1185-91
JournalNucleic Acids Research
Volume41
Issue numberDatabase issue
DOIs
Publication statusPublished - 1 Jan 2013

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Arabidopsis Proteins
Databases
Proteins
Cell Compartmentation
Bayes Theorem
Plant Cells
Green Fluorescent Proteins
Organelles
Proteomics
Hot Temperature

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abstract = "The subcellular location database for Arabidopsis proteins (SUBA3, http://suba.plantenergy.uwa.edu.au) combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization and protein-protein interaction (PPI) datasets with subcellular targeting calls from 22 prediction programs. More than 14 500 new experimental locations have been added since its first release in 2007. Overall, nearly 650 000 new calls of subcellular location for 35 388 non-redundant Arabidopsis proteins are included (almost six times the information in the previous SUBA version). A re-designed interface makes the SUBA3 site more intuitive and easier to use than earlier versions and provides powerful options to search for PPIs within the context of cell compartmentation. SUBA3 also includes detailed localization information for reference organelle datasets and incorporates green fluorescent protein (GFP) images for many proteins. To determine as objectively as possible where a particular protein is located, we have developed SUBAcon, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein's location in the cell. The probabilities of subcellular location for each protein are provided and displayed as a pictographic heat map of a plant cell in SUBA3.",
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SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. / Tanz, Sandra K; Castleden, Ian; Hooper, Cornelia M; Vacher, Michael; Small, Ian ; Millar, A Harvey.

In: Nucleic Acids Research, Vol. 41, No. Database issue, 01.01.2013, p. D1185-91.

Research output: Contribution to journalArticle

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