SAMMD: Staphylococcus aureus microarray meta-database

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.

Figure 1

SAMMD Data Informatics.

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.

Figure 3

Output of a simple search in SAMMD using a Gene name. "sarA" has been used as a query term in this search. Clicking on the ORF ID would pull out its transcriptomic status in SAMMD, after mapping it to N315 ID.

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.

Figure 5

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

Figure 6

Venn diagram showing the results of comparing three datasets. Clicking on the numbers in the Venn diagram shows the corresponding list of genes in a pop up window.