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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #206274

Title: Development of soybean gene expression database (SGED)

item Clough, Steven

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2006
Publication Date: 1/17/2007
Citation: Li, M., Cai, Y., Clough, S.J. 2007. Development of soybean gene expression database (SGED). Plant and Animal Genome XV Conference. p. 313.

Interpretive Summary:

Technical Abstract: Large volumes of microarray expression data is a challenge for analysis. To address this problem a web-based database, Soybean Expression Database (SGED) was built, using PERL/CGI, C and an ORACLE database management system. SGED contains three components. The Data Mining component serves as a repository for normalized gene expression data derived from soybean cDNA microarray studies, experimental design and array information. Web applications have been developed for cross comparison or retrieving data from multiple projects. Additionally, some analysis tools were developed. The Gene Information component serves as an information warehouse pertaining to all spots on the cDNA slides from the lab at the University of Illinois as well as Affymetrix soybean expression chips. Information includes microarray gene identifiers, annotations from NCBI and TIGR, as well as the ability to identify which cDNA spots best match a given gene probe set on the Affymetrix chip to allow comparing soybean cDNA array data to that of Affymetrix soybean chip data. Web interfaces have been built for information retrieval. Users may cut and paste or upload gene lists and search for a variety of annotation options such as Microarray clone ID, TIGR TC, GO terms and functional information. The database is also searchable by keyword which can be restricted to searches of individual print sets. Thirdly, SGED will contain raw and normalized digital expression (EST abundance) data derived from analysis of the complete public soybean EST collection obtained from 120 different non-normalized EST libraries. The current URL is