Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 23, 2003
Publication Date: October 23, 2003
Citation: Alkharouf, N., Matthews, B.F. 2003. Sgmd: the soybean genomics and microarray database.. Nucleic Acids Research. 32:D398-D400.
Interpretive Summary: There has been a tremendous increase in the amount of molecular data related to soybean due to high-throughput DNA sequencing and gene expression projects. These data need to be well organized, readily accessible, and easily searched to be highly useful. We established the Soybean Genomics and Microarray Database (SGMD), that contains DNA sequences of soybean and soybean cyst nematode genes, gene expression data using microarray data, and other useful information about soybean and the soybean cyst nematode. This database is accessible on-line via the computer at: http://psi081.ba.ars.usda.gov/SGMD/default.htm. SGMD provides scientists with an integrated view of the interaction of soybean with the soybean cyst nematode. The database contains analytical tools on-line that allow immediate analysis and searching of microarray data which is much faster than requiring the user to download data files and analyze the data using separate software programs. SGMD is completely accessible and scientists can use this database for analysis of the interactions of soybean with the soybean cyst nematode.
The Soybean Genomics and Microarray Database (SGMD) attempts to provide an integrated view of the interaction of soybean with the soybean cyst nematode and contains genomic, EST, and microarray data with embedded analytical tools allowing correlation of soybean ESTs with their gene expression profiles. SGMD provides analytical tools to mine the microarray data quickly by integrating many analysis methods within the database itself. The expression profiles of genes at time intervals during the first eight days of nematode invasion is searchable by gene name or Genbank accession number. Recent developments include the addition of a searchable database for soybean cyst nematode ESTs and photographs of the invasion process at time points examined using microarrays. SGMD is completely accessible from the web at: http://psi081.ba.ars.usda.gov/SGMD/default.htm.