University of Oulu

Cornelia M. Hooper, Ian R. Castleden, Sandra K. Tanz, Nader Aryamanesh, A. Harvey Millar, SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D1064–D1074, https://doi.org/10.1093/nar/gkw1041

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

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Author: Hooper, Cornelia M.1; Castleden, Ian R.1; Tanz, Sandra K.1;
Organizations: 1ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
2Department of Genetics and Physiology, Biocenter Oulu, FIN-90014 University of Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 4.8 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe202103248180
Language: English
Published: Oxford University Press, 2016
Publish Date: 2016-11-24
Description:

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.

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Series: Nucleic acids research
ISSN: 0305-1048
ISSN-E: 1362-4962
ISSN-L: 0305-1048
Volume: 45
Issue: D1
Pages: D1064 - D1074
DOI: 10.1093/nar/gkw1041
OADOI: https://oadoi.org/10.1093/nar/gkw1041
Type of Publication: A1 Journal article – refereed
Field of Science: 1182 Biochemistry, cell and molecular biology
Subjects:
Funding: ARC Centre of Excellence in Plant Energy Biology [CE140100008]. Funding for open access charge: ARC Centre of Excellence in Plant Energy Biology. Conflict of interest statement. None declared.
Copyright information: © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  https://creativecommons.org/licenses/by/4.0/