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Introduction

The Lotus japonicus Gene Expression Atlas (LjGEA) Project
Gene Chip Lotus japonicus is a wild perennial legume that has been developed as a model or reference species for legume genetics, genomics, and breeding. To aid in determining the functions of each individual gene in the recently published L. japonicus genome [1], we have developed an "atlas" of gene expression profiles for the majority of L. japonicus genes covering all its major organ systems (leaves, petioles, stem, roots, nodules, flowers, seeds and seed pods) with a detailed developmental time-series for seeds and seed pods, using the Affymetrix Lotus GeneChip ®. In the future, these data are expected to include cell and tissue specific transcriptome data as well as data from plants subjected to various stress conditions contributed by the scientific community. With the recently generated Medicago Gene Expression Atlas [2], we anticipate that these data will aid gene function discovery and molecular breeding efforts in legumes.

The complete dataset 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 Lotus 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 Lotus japonicus 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,
For questions and suggestions regarding the web server, please contact



Citation(s)
  1. Jerome Verdier, Ivone Torres-Jerez, Mingyi Wang, Andry Andriankaja, Stacy N. Allen, Ji He, Yuhong Tang, Jeremy D. Murray, Michael K. Udvardi1,"Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation". The Plant Journal, 2013 (dpi 10.1111/tpj.12119)

News & Service Updates
[2013/05/20] Check out our new comparative gene regulatory network (GRN) server: LegumeGRN (http://legumegrn.noble.org) provides the community web services 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 across multiple species. Three species are available, namely Medicago, Lotus and soybean.

[2012/09/30] Release of public version of LjGEA.

[2009/02/02] Restricted external access: Invited external collaborators may access LjGEA using provide user name and password now. GO annotations, KEGG annotations and transcription factor families are yet to be loaded. All other databases and analytical modules are functioning.

[2008/10/22] What are available for now: All databases except for GO annotations, KEGG annotations and transcription factor families are loaded. When you search, please do make sure you set "Limit probesets in" option to "All: Mtr, Msa, Sme and controls" -- this is a piece of "legacy" software code transfered from the Medicago Gene Expression Atlas that is pending clean-up. If you choose "Mtr only", you'll get nothing.

[2008/09/03] First version: This is a quick cloning of the MtGEA with minimal code tweaking. The primary expression and presence/absence calls tables are currated now. All other data to be populated soon.
 
         
       
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