SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis
Open Access
- 23 November 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 41 (D1), D1185-D1191
- https://doi.org/10.1093/nar/gks1151
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.This publication has 43 references indexed in Scilit:
- Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificityProceedings of the National Academy of Sciences of the United States of America, 2012
- The Arabidopsis Information Resource (TAIR): improved gene annotation and new toolsNucleic Acids Research, 2011
- The IntAct molecular interaction database in 2012Nucleic Acids Research, 2011
- AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope ProteinsMolecular & Cellular Proteomics, 2010
- YLoc—an interpretable web server for predicting subcellular localizationNucleic Acids Research, 2010
- Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thalianaMolecular Systems Biology, 2010
- The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation ProgramJournal of Proteomics, 2009
- AmiGO: online access to ontology and annotation dataBioinformatics, 2008
- WoLF PSORT: protein localization predictorNucleic Acids Research, 2007
- SUBA: the Arabidopsis Subcellular DatabaseNucleic Acids Research, 2006