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Bioinformatics Advance Access originally published online on March 7, 2007
Bioinformatics 2007 23(11):1418-1423; doi:10.1093/bioinformatics/btm040
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

MedicCyc: a biochemical pathway database for Medicago truncatula

Ewa Urbanczyk-Wochniak and Lloyd W. Sumner *

The Samuel Roberts Noble Foundation, Inc., Ardmore, OK 73401, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: There is an imperative need to integrate functional genomics data to obtain a more comprehensive systems-biology view of the results. We believe that this is best achieved through the visualization of data within the biological context of metabolic pathways. Accordingly, metabolic pathway reconstruction was used to predict the metabolic composition for Medicago truncatula and these pathways were engineered to enable the correlated visualization of integrated functional genomics data.

Results: Metabolic pathway reconstruction was used to generate a pathway database for M. truncatula (MedicCyc), which currently features more than 250 pathways with related genes, enzymes and metabolites. MedicCyc was assembled from more than 225 000 M. truncatula ESTs (MtGI Release 8.0) and available genomic sequences using the Pathway Tools software and the MetaCyc database. The predicted pathways in MedicCyc were verified through comparison with other plant databases such as AraCyc and RiceCyc. The comparison with other plant databases provided crucial information concerning enzymes still missing from the ongoing, but currently incomplete M. truncatula genome sequencing project. MedicCyc was further manually curated to remove non-plant pathways, and Medicago-specific pathways including isoflavonoid, lignin and triterpene saponin biosynthesis were modified or added based upon available literature and in-house expertise. Additional metabolites identified in metabolic profiling experiments were also used for pathway predictions. Once the metabolic reconstruction was completed, MedicCyc was engineered to visualize M. truncatula functional genomics datasets within the biological context of metabolic pathways.

Availability: freely accessible at http://www.noble.org/MedicCyc/

Contact: lwsumner{at}noble.org

Associate Editor: Alex Bateman

Received on October 26, 2006; revised on January 29, 2007; accepted on February 1, 2007

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