Abstract
BackgroundStaphylococcus 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 users to perform a variety of analysis against and within the existing transcriptional profiles.DescriptionSAMMD 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 holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the 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, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL).ConclusionSAMMD is hosted and available at . Currently there are over 9500 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.
Highlights
Staphylococcus aureus is an important human pathogen, causing diseases ranging from superficial skin infections to severe life threatening infections
The use of this large amount of expression data is limited by the fact that it is not located in a centralized source. Those data that have been deposited in the public databases are difficult to use for direct comparisons to data generated by researchers. We have addressed this issue by building a Staphylococcus aureus microarray meta-database (SAMMD) which contains all the published microarray data generated for S. aureus
Clicking on the ORF ID would pull out its transcriptomic status in Staphylococcus aureus Microarray meta-database (SAMMD), after mapping it to N315 ID
Summary
Importance and relevance of the database Microarray gene expression databases like NCBI-GEO and EBI-ArrayExpress hold the raw data only for a very few of the 30 published Microarray papers that are listed in OFiugtupruet o2f a simple search in SAMMD using an ORF ID Output of a simple search in SAMMD using an ORF ID. SAMMD is a searchable database of Microarray gene expression data of S. aureus. Such a database is valuable in staphylococcal research in light of increasing multipleantibiotic resistance in S. aureus. JavaScript based pop-up windows are used to display some of the data in SAMMD, so the users should have JavaScript enabled their browsers for the full functionality of the database.
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