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      Medicago truncatula Gene Expression Atlas  
 
     
Introduction

The Medicago truncatula Gene Expression Atlas (MtGEA) 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 can be downloaded from ArrayExpress, where complete MIAME information is also deposited.



The Medicago truncatula Gene Expression Atlas (MtGEA) Web Server
The Medicago truncatula Gene Expression Atlas (MtGEA) Web Server is developed to maximize the use of publicly-available Affymetrix GeneChip data and aid efforts to "interpret" the Medicago genome through functional genomics. This web server aims to archive all publically-available M. truncatula gene expression data derived from the use of the Affymetrix GeneChip.

The web 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, KEGG bincode or protein domain name) as starting point. The web server also seamlessly inter-connects with our Mt genome browser, which allows the user to query using various genomics features (e.g. a particular chromosome coordinate or an EST ID mapped to the genome) and links back to the corresponding expression profiles in MtGEA. 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.

In this new version of MtGEA v2, we have included not only all the above-mentioned MtGEA project data (60 chips from 20 experiments), but also a large number of publically available data based the same Medicago GeneChip (96 chips from 44 experiments), thus almost tripled the database size (156 chips from 64 experiments in total). Details of these data can be found in our slides customization page, whereas the citations to these data can be found in our references page. Our slides customization utility allows you to select a flexible subset of the gene expression data in your search and analysis session.

Visitors shall note that gene expression data in this new version have been renormalized. Thus the subset of the MtGEA project data downloaded from this version will have different signal readings from the initial version (all readings are linearly scaled, though). If you prefer using the MtGEA data from the initial version, please click here.

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).

Current development on the MtGEA web server on gene regulatory network (GRN) prediction and visualization is supported by the Oklahoma Center for the Advancement of Science & Technology (OCAST) Oklahoma Plant Science Research (OPSR) program. The GRN prediction pipeline is planned for public release in the Spring of 2012.

For overall questions and collaboration opportunities regarding the MtGEA project, please contact the principle investigator of the project, For questions and suggestions regarding the MtGEA Web Server, please contact



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, 55(3):504--513.
  2. Ji He, Vagner A. Benedito, Mingyi Wang, Jeremy D. Murray, Patrick X. Zhao, Yuhong Tang and Michael K. Udvardi. "The Medicago truncatula gene expression atlas web server". BMC Bioinformatics. 2009, 10:441



News & Service Updates
[2012/07/20] Check out our new comparative gene regulatory network (GRN) server: LegumeGRN (http://legumegrn.noble.org) provides the community software tools for predicting GRNs based on the gene expression profiles we have curated, visualization interface for inspection of GRNs and query for genes of interests, and comparative functions even across multiple species. Three species are available, namely Medicago, Lotus and soybean. -- http://legumegrn.noble.org.

[2011/10/29] Updated Mt 3.5 annotation: We have updated the probeset-gene mapping using the latest Mt 3.5 gene set.

[2011/03/01] OCAST OPSR proposal funded: Our proposal on development of gene regulatory network (GRN) prediction pipeline has been funded by OCAST. We expect to have the prediction pipeline ready for public access in the spring of 2012, and a set of pre-curated GRNs surrounding Medicago transcription factors by the spring of 2013.

[2010/09/09] MtGEA V3 in the plan: We are planning on a major update of the MtGEA. Work on the V3 will be primarily focused on curation of new publiclly available microarray chips. We welcome your inputs and recommendations for us to complie a full list of lately published chips since V2. Please email to jhe_at_noble_dot_org.

[2010/05/19] MtGEA dedicated host: We have relocated the MtGEA server to a dedicate VM host http://mtgea.noble.org. Please update your bookmark. Please report any server related problem to jhe_at_noble_dot_org.

[2009/07/10] MtGEA V2: We are pleased to announce the 2nd major release of the MtGEA web server. In this version, we have tripled the gene expression data size (see "slides customization" page for more details). We have also added a number of new annotation data sets and new software features to improve your utilization of the web services. These include, but are not limited to, (1) a new set of transcription factors predicted based on Arabidopsis homologs; (2) a new set of GO annotations, also based on Arabidopsis homologs; (3) protein domain information based on InterProScan searches; (4) a "slides customization" page that allows you to choose a dynamic subset of gene expression data in your search and analysis session; and (5) an improved "multi-transcript viewer" that allows you to visualize and compare multiple gene expression profiles in the same chart. Check out the links marked with and signs, and don't hesitate to contact us if you have any comments and suggestions!
 
         
       
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