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Introduction

The Medicago truncatula Gene Expression Atlas Project
Gene Chip Medicago truncatula is a model or reference species for legume genetics, genomics, and breeding. To leverage the genome sequencing that is currently being done for this species, we have developed a compendium or "atlas" of gene expression profiles for the majority of M. truncatula genes covering all its major organ systems (roots, nodules, stems, petioles, leaves, vegetative buds, flowers, seeds and seed pods) with detailed developmental time-series for nodules and seeds, using the Affymetrix Medicago Gene Chip ®. In the future, these data will be supplemented with transcriptome data from plants subjected to various kinds of abiotic and biotic stresses and data from specific cell and tissue types. We anticipate that these data will aid gene function determination, biological discovery, and molecular breeding efforts.

The complete dataset behind this web service can be downloaded from ArrayExpress, where complete MIAME information is also deposited.



This Web Server
The service provided here allows the user to identify and analyze the expression of one or more genes of interest, using the Affymetrix Medicago probe-set identification number, gene sequence, gene annotation information (such as gene ID, keyword in description, GO term or KEGG bincode) as starting point. The user may further study gene expression profiles based on co-expression analysis and differential expression analysis. The user may also directly download the whole dataset organized by experiment. Data output can be selected by the user and is provided in a tabular form compatible with common analytical and visualization software.

This service is under development to extend the range of data and processing options, and we welcome suggestions for additional services that could be provided to improve data mining and knowledge generation.



Funding Support and Contact
The Medicago truncatula Gene Expression Atlas project is supported by the National Research Initiative (NRI) Plant Genome Program of the USDA Cooperative State Research, Education and Extension Service (CSREES).

For overall questions and collaboration opportunities, please contact the principle investigator of the project,



Citation(s)
  1. Vagner Benedito, Ivone Torez-Jerez, Jeremy Murray, Andry Andriankaja, Stacey Allen, Klementina Kakar, Maren Wandrey, Jerome Verdier, Helene Zuber, Thomas Ott, Sandra Moreau, Andreas Niebel, Tancred Frickey, Georg Weiller, Ji He, Xinbin Dai, Patrick Zhao, Yuhong Tang, and Michael Udvardi. "A gene expression atlas of the model legume Medicago truncatula". The Plant Journal. 2008. Accepted for publication.



News & Service Updates
[2008/07/02] Performance Degradation: We are aware of some slowing-down of the gene atlas database. This is caused by a recent hardware failure of our ISP, which is affecting both inbound and outbound network connections of the entire institute. Thank you for reporting this problem to us. And we appreciate your patience. 		 
         
       
© 2008 by The Samuel Roberts Noble Foundation, Inc.