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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
AraCyc: a biochemical pathway database for Arabidopsis
Lukas A Mueller1, Peifen Zhang, Seung Y Rhee
1The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford 94305, USA. mueller@acoma.stanford.edu
Plant Physiology
|June 14, 2003
Summary
AraCyc is a comprehensive database detailing Arabidopsis biochemical pathways. It offers a user-friendly interface for exploring plant metabolism, including over 170 pathways and plant-specific metabolic routes.
Area of Science:
- * Plant biology
- * Biochemistry
- * Bioinformatics
Background:
- * The Arabidopsis Information Resource (TAIR) developed the AraCyc database.
- * AraCyc aims to comprehensively represent Arabidopsis thaliana metabolism.
- * It provides a user-friendly web interface for accessing metabolic information.
Purpose of the Study:
- * To create a detailed database of Arabidopsis biochemical pathways.
- * To enable visualization of metabolic pathways and compound structures.
- * To facilitate access to plant metabolic data for researchers.
Main Methods:
- * Utilized Pathway Tools software, including the Pathologic module.
- * Employed MetaCyc as a reference database for initial construction.
- * Manually refined and annotated pathways, incorporating literature data.
- * Developed PerlCyc for programmatic access to the database.
Main Results:
- * Features over 170 biochemical pathways for Arabidopsis.
- * Includes detailed information on compounds, genes, proteins, and subcellular locations.
- * Integrated over 20 plant-specific pathways (e.g., carotenoid, brassinosteroid, gibberellin biosynthesis).
- * Quality assessment compared automated builds with manually curated versions.
Conclusions:
- * AraCyc provides a valuable resource for studying Arabidopsis metabolism.
- * The database integrates diverse metabolic information with user-friendly visualization tools.
- * Ongoing expansion will include additional plant pathways.
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