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Nucleic Acids Res. 2017 Jan 4;45(D1):D1064-D1074. doi: 10.1093/nar/gkw1041. Epub 2016 Nov 28.

SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations.

Author information

1
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia cornelia.hooper@uwa.edu.au.
2
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia.
3
Department of Genetics and Physiology, Biocenter Oulu, FIN-90014 University of Oulu, Finland.

Abstract

The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations. The new SUBA4 user interface enables users to choose quickly from the filter categories: 'subcellular location', 'protein properties', 'protein-protein interaction' and 'affiliations' to build complex queries. This allows substantial expansion of search parameters into 80 annotation types comprising 1 150 204 new annotations to study metadata associated with subcellular localization. The 'BLAST' tab contains a sequence alignment tool to enable a sequence fragment from any species to find the closest match in Arabidopsis and retrieve data on subcellular location. Using the location consensus SUBAcon, the SUBA4 toolbox delivers three novel data services allowing interactive analysis of user data to provide relative compartmental protein abundances and proximity relationship analysis of PPI and coexpression partners from a submitted list of Arabidopsis gene identifiers.

PMID:
27899614
PMCID:
PMC5210537
DOI:
10.1093/nar/gkw1041
[Indexed for MEDLINE]
Free PMC Article

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