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Title: SMGD: THE SOYBEAN GENOMICS AND MICROARRAY DATABASE

Author
item ALKHAROUF, NADIM - GEORGE MASON UNIVERSITY
item Matthews, Benjamin - Ben

Submitted to: Mid Atlantic Plant and Molecular Biology Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 6/30/2001
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The soybean genomics and microarray database was established in 1999 to serve as a sequence and microarray database for the Soybean Genomics and Improvement Laboratory (SGIL), Beltsville Agricultural Research Center (BARC) and collaborators. It serves both as a sequence repository, holding DNA sequences for numerous EST's, and also as a microarray experiment database. It allows scientists to explore the expression levels of the EST clones stored in the database and to correlate expression levels with function. SGMD is a relational database built on SQLServer2000 and incorporates the minimal information about a microarray experiment (MIAME) guidelines set forth by the microarray gene expression database (MGED) group. This ensures that the data can be interpreted and used following certain set standards. It also provides appropriate, complete information for other scientists to verify the data. Web interfaces have been developed for the database, whereby numerous statistical analyses, such as one-way analysis of variance (ANOVA) and T-tests can be performed on the fly from any web browser. Web interfaces also have been developed for complex comparison queries, allowing scientists to correlate and find similarities and differences across different experiments and probe combinations. This is all accomplished without the need to resort to third party software. Everything is handled by the use of SQL procedures within the database itself. Thus SGMD not only serves as a database, but as a data analysis tool as well, which makes it unique to most other microarray databases.