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.
Highlights
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) has grown into a substantial collection of manually curated published data sets of largescale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI), subcellular targeting calls from 22 prediction programs as well as a consensus algorithm.The database originated from studies on the mitochondrial proteome >10 years ago [1]
Such analysis prompted the generation of the Arabidopsis Mitochondrial Protein Database (AMPDB) that offered an overview of the detailed mass spectrometry (MS) data sets from 17 published mitochondrial studies as well as predictions from 6 subcellular location algorithms [2]
Each tool provides a unique link between the subcellular location consensus (SUBAcon) and protein abundance (MMAP), coexpression (CAT) and PPI (PAT) data, respectively, giving the SUBA4 user straightforward data analysis options
Summary
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) has grown into a substantial collection of manually curated published data sets of largescale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI), subcellular targeting calls from 22 prediction programs as well as a consensus algorithm. Untangling which proteins were associated with mitochondrial functions and localized in mitochondria and which were low-level contaminants in purified mitochondrial preparation became a priority to resolve Such analysis prompted the generation of the Arabidopsis Mitochondrial Protein Database (AMPDB) that offered an overview of the detailed MS data sets from 17 published mitochondrial studies as well as predictions from 6 subcellular location algorithms [2]. SUBA has contributed to the development of widely used organelle marker sets [11], protein family clone collections for functional genomics [12], as well as facilitated the functional elucidation of protein families involved in plant growth regulation [13] The latter resources and knowledge were used in over 900 downstream studies. This creates a new integrated SUBA data analysis centre that enriches SUBA data analysis options, discoverability as well as the re-use of published data derived from global experimental and computational efforts
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