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SAMMD: Staphylococcus aureus Microarray Meta-Database.Nagarajan V, Elasri MO
ABSTRACT: BACKGROUND: Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps to perform comparative studies of transcriptional profiles. SAMMD also allows the user to use ORF IDs to search for all the regulatory mutants or growth conditions in which the query gene's expression is altered. Description SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which hold information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, advanced search, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL). CONCLUSIONS: SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. Currently there are over 9000 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes. Published 3 October 2007 in BMC Genomics, 8(1): 351.
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