SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis
By Sandra K. Tanz, I. Castleden, C. Hooper, M. Vacher, Ian Small, Harvey A. Millar. Nucleic Acids Res., 2012
305 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/443769ca7014ad73659d81f39191640ae732c53e
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In Molecular Biology
- Michael J.E. Sternberg
- Lawrence A. Kelley
- Sune Frankild
- Janos X. Binder
- Kalliopi Tsafou
- Lars Juhl Jensen
- Nicholas J. Provart
- Reinhard Schneider
In Spectroscopy
Citations in the corpus
- ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology[OPEN] (2017, methodology): “The data for this module/view originate from SUBA3 database (Tanz et al., 2013) via a web service hosted by the BAR.”
- SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations (2016, methodology): “(B) The accumulative citation record of the SUBA database based on SUBA1(4), SUBA2(5), SUBA3(6) and SUBAcon(7) reports between 2005 and 2015.”
- COMPARTMENTS: unification and visualization of protein subcellular localization evidence (2014, methodology): “An exception is the A. thaliana resource SUBA3, which assigns an overall confidence score; however, it is difficult for the user to trace these scores back to their origin.”