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

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.

Figure 1.

SUBA use in plant biology research. (A) The increase of collated localization data and coverage of the Arabidopsis proteome in SUBA releases from 2005 to 2016. (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. Impact of SUBA data on (C) Plant biology research areas and (D) species-specific discoveries given as parts of retrieved studies that have cited SUBA.

Figure 2.

SUBA4 curation, calculations, predictions, classifications data and interrogation overview. The SUBA4 data collation (top) is accessible through the interface (middle). The interface offers the query platform (bottom left) for filtering data and the toolbox (bottom right) for rapid statistics. ASURE—Arabidopsis SUbcellular REference, CoEx—coexpression, FP—fluorescent protein, MS—mass spectrometry, PPI—protein–protein interaction.

Figure 3.

SUBA4 query platform overview. Each query category is summarized in a green box (top) indicating individual filter options. The filters from each category can be linked into one main query using Boolean AND/OR terms as indicated in the red box (bottom). FP—fluorescent protein, MS—mass spectrometry, PPI—protein–protein interaction.

Figure 4.

SUBA4 MMAP tool overview. The MMAP tool in the toolbox tab accepts lists or text containing AGIs in the top window (top panel). The MMAP tool returns summarized counts of protein species per compartment as well as the relative protein abundance estimation per compartment (middle panel). The bottom panel returns an enrichment factor relative to the expected compartmental protein abundance distribution in green or other tissues. MMAP—Multiple Marker Abundance Profiling.

Figure 5.

SUBA4 Coexpression Adjacency Tool (CAT) overview. The CAT accepts lists or text containing AGIs in the top and allows filter options for coexpression strength and proximity relationships of proteins derived from coexpressed genes (top panel). The submit button allows to ‘find coexpressed proteins’ for all AGIs or to narrow coexpression partners to within the submitted AGI list. More filter options in CAT allow specifying subcellular locations of AGIs in the submitted list as well as the returned coexpression partners (middle panel). The tool returns a protein type distribution for proteinA and proteinB as well as the distribution of proximity relationships (match, adjacent, distant, secretory) within a submitted list or associated with a submitted list (bottom panel). The distributions are returned as relative bar charts and pie charts.