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. 2009 Nov 11;10:517.
doi: 10.1186/1471-2164-10-517.

An Expression Database for Roots of the Model Legume Medicago Truncatula Under Salt Stress

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Free PMC article

An Expression Database for Roots of the Model Legume Medicago Truncatula Under Salt Stress

Daofeng Li et al. BMC Genomics. .
Free PMC article

Abstract

Background: Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes.

Description: The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database.

Conclusion: MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.

Figures

Figure 1
Figure 1
Functional category enrichment analysis of differentially expressed probe sets at different time points based on GeneBins Ontology. Up-regulated or Down-regulated means expression of probe sets at one time point changed more or less than 2 fold versus 0 hour, respectively, and p-value < 0.05.
Figure 2
Figure 2
Overlap of early-induced (a) and recovery-related (b) genes in a previous report between probe sets that significant up-regulate more than 2 fold at each time point. Note: the numbers of probe sets identified as early-induced and recovery-related after salt stress in our work were different from the numbers reported in the previous study; this is because the version of the Medicago truncatula sequence release has been changed.

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