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United States Department of Agriculture

Agricultural Research Service

Title: Development of a soybean gene expression database to cross compare microarray experiments

Authors
item Li, Min - UNIV OF ILLINOIS
item Calla, Bernarda - UNIV OF ILLINOIS
item Zhu, Jin - UNIV OF ILLINOIS
item Cai, Dora - UNIV OF ILLINOIS
item Clough, Steven

Submitted to: International Congress on Molecular Plant-Microbe Interactions
Publication Type: Abstract Only
Publication Acceptance Date: February 27, 2007
Publication Date: July 21, 2007
Citation: Li, M., Calla, B., Zhu, J., Cai, D., Clough, S.J. 2007. Development of a soybean gene expression database to cross compare microarray experiments. International Congress on Molecular Plant-Microbe Interactions. July 21-27, 2007. Sorrento, Italy. p. 324.

Technical Abstract: Microarrays are a revolutionary tool to estimate expression levels of genes within an organism. In a fairly quick and simple experiment, one can monitor expression of tens of thousands of genes. The relative ease of use and availability of array platforms for many commonly researched plants, is generating massive amounts of valuable expression data. To assist with the analysis of soybean expression experiments, we used PERL/CGI, C and an ORACLE database management system to develop a web-accessible, public Soybean Gene Expression Database (SGED) with several useful features. SGED contains searchable annotations from NCBI, TIGR and TAIR for all genes represented on soybean cDNA from the University of Illinois as well as from Affymetrix soybean expression chips. A BLAST server will search and parse top hits for nearest match within soybean ESTs and TCs that are represented on soybean cDNA slides. Data querying and clustering tools can analyze expression data with p-values and fold changes from published projects from the Clough lab (will add outside experiments in future). All output files and tables are down-loadable. SGED is housed at the National Center for Supercomputing Applications at the University of Illinois (http://aragon.ncsa.uiuc.edu/soybean-microbe). We plan to expand the BLAST feature to include sequence databases for other plant expression arrays such as Medicago, Lotus, and Arabidopsis to allow identification of best matches across different plant arrays and cross comparison to soybean projects. Examples will be shown cross comparing expression data from soybean treated with Pseudomonas syringae, Sclerotinia sclerotiorum, Fusarium solani, Bradyrhizobium japonicum, and herbicide.

Last Modified: 10/30/2014
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