MedicCyc: a biochemical pathway database for Medicago truncatula
Ewa Urbanczyk-Wochniak1, Lloyd W Sumner
1The Samuel Roberts Noble Foundation, Inc., Ardmore, OK 73401, USA.
Bioinformatics (Oxford, England)
|March 9, 2007
Summary
A new database, MedicCyc, was created for Medicago truncatula to visualize functional genomics data within metabolic pathways. This systems biology approach integrates genomic information for a comprehensive understanding of plant metabolism.
Area of Science:
- Plant Systems Biology
- Functional Genomics
- Metabolic Pathway Engineering
Background:
- Integrating functional genomics data is crucial for a comprehensive systems biology understanding.
- Visualizing this data within the context of metabolic pathways is an effective approach.
- Metabolic pathway reconstruction aids in predicting and understanding plant metabolic composition.
Purpose of the Study:
- To reconstruct metabolic pathways for Medicago truncatula.
- To engineer these pathways for visualizing integrated functional genomics data.
- To create a comprehensive systems biology view of Medicago truncatula.
Main Methods:
- Metabolic pathway reconstruction using Pathway Tools and MetaCyc database.
- Assembly from Medicago truncatula ESTs and genomic sequences.
- Manual curation and integration of literature and experimental data.
Main Results:
- MedicCyc database developed with over 250 pathways for M. truncatula.
- Database assembled from >225,000 ESTs and genomic sequences.
- Verified pathways and identified missing enzymes through comparison with AraCyc and RiceCyc.
Conclusions:
- MedicCyc enables visualization of functional genomics data in a biological context.
- The database aids in understanding Medicago truncatula's metabolic capabilities.
- MedicCyc is a valuable resource for plant systems biology research.
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