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

Area of Science:

• Plant Biology
• Proteomics
• Bioinformatics

Background:

• Subcellular localization is crucial for protein function in plants.
• Existing databases often lack comprehensive, manually curated experimental data.
• Understanding protein-protein interactions (PPI) and localization is key to plant cell biology.

Purpose of the Study:

• To present SUBA4, an updated and expanded database for Arabidopsis protein subcellular localization.
• To integrate diverse data types including proteomics, fluorescent visualization, and PPI data.
• To provide enhanced tools for querying and analyzing protein localization and interaction data.

Main Methods:

• Manual curation of published large-scale subcellular proteomics and PPI datasets.
• Inclusion of data from 22 prediction programs for subcellular targeting.
• Development of a new user interface with advanced filtering and a BLAST search tool.
• Integration of a location consensus tool (SUBAcon) for data analysis.

Main Results:

• SUBA4 now contains over 60,000 experimental protein location claims and 37 new suborganellar categories.
• Expanded PPI data includes 26,327 pairs, with 856 localized via fluorescent visualization.
• The database incorporates 1,150,204 new annotations across 80 types, enabling complex queries.
• New data services offer interactive analysis of protein abundance and PPI/coexpression relationships.

Conclusions:

• SUBA4 provides a significantly enhanced resource for studying Arabidopsis protein localization and interactions.
• The integrated data and advanced tools facilitate deeper insights into plant cell organization and function.
• SUBA4 supports comparative analysis across species and aids in understanding protein behavior within the cell.