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Updated: Jun 17, 2026
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Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
Published on: January 14, 2016
AtPIN: Arabidopsis thaliana protein interaction network
Marcelo M Brandão1, Luiza L Dantas, Marcio C Silva-Filho
1Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-970 Piracicaba, SP, Brazil. mbrandao@esalq.usp.br
BMC Bioinformatics
|January 2, 2010
Summary
AtPIN is a new database for studying protein-protein interactions in Arabidopsis thaliana. It integrates interaction data, ontology, and localization, aiding in reliable network mapping.
Area of Science:
- Plant biology
- Molecular biology
- Bioinformatics
Background:
- Protein-protein interactions (PPIs) are essential for life.
- Arabidopsis thaliana is a model organism for plant research.
- Publicly available PPI datasets are valuable resources.
Purpose of the Study:
- To develop AtPIN, a database and web interface for Arabidopsis thaliana PPIs.
- To provide a tool for searching and building PPI networks.
- To integrate PPI data with ontology and sub-cellular localization information.
Main Methods:
- Collected and curated publicly available PPI datasets for Arabidopsis thaliana.
- Developed a database and web interface (AtPIN) for data access and analysis.
- Implemented a cellular compartment classification (C3) system for PPIs.
- Utilized Functional Similarity Weight (FSW) to assess PPI reliability.
- Combined AtPIN search with yeast two-hybrid screening to identify target proteins.
Main Results:
- AtPIN categorizes PPIs into experimentally demonstrated or predicted.
- The Functional Similarity Weight (FSW) aids in postulating PPI reliability.
- AtPIN predicted target proteins for cytosolic glutamyl-tRNA synthetase (Cyt-gluRS).
- Experimental screening validated AtPIN's predictions for Cyt-gluRS targets.
Conclusions:
- AtPIN is a user-friendly tool for Arabidopsis thaliana PPI analysis.
- The database integrates PPIs, ontology, and sub-cellular localization.
- AtPIN offers a reliable strategy for mapping protein-protein interactions in Arabidopsis.
- The tool is accessible at http://bioinfo.esalq.usp.br/atpin.
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