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PMID: 23180787 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 41 ·No. Database issue ·2013-01-00 ·Pages D1185-91

Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA

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.

MeSH Terms
Arabidopsis Proteins/analysis Databases, Protein Internet Protein Interaction Mapping Proteomics Systems Integration User-Computer Interface
Chemicals
Arabidopsis Proteins
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Tanz Sandra K
Centre of Excellence in Computational Systems Biology, The University of Western Australia, Perth, WA 6009, Australia.
Castleden Ian
Hooper Cornelia M
Vacher Michael
Small Ian
Millar Harvey A
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gks1151
Published
2013-01-00
Epub
2012-00-24
Pages
D1185-91
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3531127
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gks1151 PMC Full Text View journal details
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