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SAMMD: Staphylococcus aureus microarray meta-database.

Nagarajan V, Elasri MO - BMC Genomics (2007)

Bottom Line: 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).It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences; The University of Southern Mississippi, MS, 39406, USA. vijayaraj.nagarajan@usm.edu

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 users to perform a variety of analysis against and within the existing transcriptional profiles.

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 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).

Conclusion: SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. 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.

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Related in: MedlinePlus

Output of a simple search in SAMMD using an ORF ID. ORF ID "SA1007" has been used as a query term in this search. All terms in the output are hyperlinked to further information.
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Figure 2: Output of a simple search in SAMMD using an ORF ID. ORF ID "SA1007" has been used as a query term in this search. All terms in the output are hyperlinked to further information.

Mentions: A powerful search tool provided in the home page of the database provides users the ability to search for the transcriptomic status of a particular gene (Figure 2). Users can search using an ORF ID (e.g. SA1233) or a Gene name (e.g. sarA) or a gene product name (e.g. urease). The search by ORF ID option accepts ORF IDs from any of the following six strains of S. aureus (N315, MW2, Mu50, COL, MRSA252, MSSA476) as input. After execution of the search, the user is provided with an output that lists all of the experiments or transcriptomes where the query gene is found. The output also shows how the query gene was affected by the regulatory gene or growth conditions i.e. up regulated, down regulated or not affected. For a search using a Gene name, SAMMD accepts any standard S. aureus gene name and first returns a list of ORF IDs that have similar gene name (Figure 3) from the above mentioned strains of S. aureus. Clicking on a particular ORF ID shows the transcriptomic status of that particular ORF ID (usually mapped to N315 ID) in all different transcriptomes available in SAMMD.


SAMMD: Staphylococcus aureus microarray meta-database.

Nagarajan V, Elasri MO - BMC Genomics (2007)

Output of a simple search in SAMMD using an ORF ID. ORF ID "SA1007" has been used as a query term in this search. All terms in the output are hyperlinked to further information.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2117023&req=5

Figure 2: Output of a simple search in SAMMD using an ORF ID. ORF ID "SA1007" has been used as a query term in this search. All terms in the output are hyperlinked to further information.
Mentions: A powerful search tool provided in the home page of the database provides users the ability to search for the transcriptomic status of a particular gene (Figure 2). Users can search using an ORF ID (e.g. SA1233) or a Gene name (e.g. sarA) or a gene product name (e.g. urease). The search by ORF ID option accepts ORF IDs from any of the following six strains of S. aureus (N315, MW2, Mu50, COL, MRSA252, MSSA476) as input. After execution of the search, the user is provided with an output that lists all of the experiments or transcriptomes where the query gene is found. The output also shows how the query gene was affected by the regulatory gene or growth conditions i.e. up regulated, down regulated or not affected. For a search using a Gene name, SAMMD accepts any standard S. aureus gene name and first returns a list of ORF IDs that have similar gene name (Figure 3) from the above mentioned strains of S. aureus. Clicking on a particular ORF ID shows the transcriptomic status of that particular ORF ID (usually mapped to N315 ID) in all different transcriptomes available in SAMMD.

Bottom Line: 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).It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences; The University of Southern Mississippi, MS, 39406, USA. vijayaraj.nagarajan@usm.edu

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 users to perform a variety of analysis against and within the existing transcriptional profiles.

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 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).

Conclusion: SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. 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.

Show MeSH
Related in: MedlinePlus