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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 an advanced search in SAMMD using a list of ORF IDs. Output shows the overlapping transcriptomes, with the corresponding list of genes. All terms in the output are hyperlinked to further information.
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Related In: Results  -  Collection

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Figure 4: Output of an advanced search in SAMMD using a list of ORF IDs. Output shows the overlapping transcriptomes, with the corresponding list of genes. All terms in the output are hyperlinked to further information.

Mentions: The advanced search lets the users to search SAMMD using a list of genes. Users can input a list of genes (any number of genes), as corresponding N315 ORF IDs. The output is the list of transcriptomes that has overlapping genes with that of the user entered gene list (Figure 4).


SAMMD: Staphylococcus aureus microarray meta-database.

Nagarajan V, Elasri MO - BMC Genomics (2007)

Output of an advanced search in SAMMD using a list of ORF IDs. Output shows the overlapping transcriptomes, with the corresponding list of genes. 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 4: Output of an advanced search in SAMMD using a list of ORF IDs. Output shows the overlapping transcriptomes, with the corresponding list of genes. All terms in the output are hyperlinked to further information.
Mentions: The advanced search lets the users to search SAMMD using a list of genes. Users can input a list of genes (any number of genes), as corresponding N315 ORF IDs. The output is the list of transcriptomes that has overlapping genes with that of the user entered gene list (Figure 4).

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