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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

Compare Datasets option. Users can compare among different datasets using this option.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2117023&req=5

Figure 5: Compare Datasets option. Users can compare among different datasets using this option.

Mentions: SAMMD users can compare two or three datasets using the "Compare" menu option (Figure 5). Comparison between datasets is performed by set operations using PHP. The results are displayed in a Venn diagram, with the numbers in the diagram linked to the list of overlapping genes (Figure 6). The SAMMD help page shows an illustration of the dataset comparison option.


SAMMD: Staphylococcus aureus microarray meta-database.

Nagarajan V, Elasri MO - BMC Genomics (2007)

Compare Datasets option. Users can compare among different datasets using this option.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Compare Datasets option. Users can compare among different datasets using this option.
Mentions: SAMMD users can compare two or three datasets using the "Compare" menu option (Figure 5). Comparison between datasets is performed by set operations using PHP. The results are displayed in a Venn diagram, with the numbers in the diagram linked to the list of overlapping genes (Figure 6). The SAMMD help page shows an illustration of the dataset comparison option.

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