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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #309396

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants

Author
item Wang, Y - University Of California
item Thilmony, Roger
item Zhao, Y - University Of California
item Chen, G - Chongqing University
item Gu, Yong

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2014
Publication Date: 11/5/2014
Citation: Wang, Y., Thilmony, R.L., Zhao, Y., Chen, G., Gu, Y.Q. 2014. AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bau117.

Interpretive Summary: Arabidopsis has been the organism of choice for many plant biochemists, physiologists, developmental biologists, and geneticists for several decades. In that time, a great deal of knowledge has been gained about the biology of this flowering plant. The availability of a broad base of knowledge about Arabidopsis and the previously developed research toolkit invites scientists to establish new techniques, develop new approaches, and test new concepts in Arabidopsis prior to their application in other species. In this study, we extracted all the Arabidopsis protein-protein interaction data in the public databases and developed a comprehensive database that provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying the protein interacting data. In addition, based on protein sequence homology search, the database developed also includes predicted protein interactions in eight other plant species (e.g. rice and maize). Therefore, this database is a powerful platform for obtaining valuable insights into the function of proteins in Arabidopsis as well as in important crops.

Technical Abstract: Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. Additionally, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL: http://probes.pw.usda.gov/AIM