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Related Experiment Video

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Microarray Analysis for Saccharomyces cerevisiae
13:17

Microarray Analysis for Saccharomyces cerevisiae

Published on: April 7, 2011

SAMMD: Staphylococcus aureus microarray meta-database.

Vijayaraj Nagarajan1, Mohamed O Elasri

  • 1Department of Biological Sciences; The University of Southern Mississippi, MS, 39406, USA. vijayaraj.nagarajan@usm.edu

BMC Genomics
|October 4, 2007
PubMed
Summary
This summary is machine-generated.

The Staphylococcus aureus Microarray meta-database (SAMMD) unifies global gene expression data from published studies. This resource aids researchers in analyzing and comparing Staphylococcus aureus transcriptional profiles to understand pathogenesis.

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A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Staphylococcus aureus is a significant human pathogen causing diverse infections and posing a public health challenge due to antibiotic resistance.
  • Understanding S. aureus pathogenesis requires analyzing global gene expression profiles, but existing data lacks a uniform annotation system.
  • Numerous transcriptional profiles have been generated, leading to a large volume of data that is difficult to comprehensively examine.

Purpose of the Study:

  • To develop a centralized, web-accessible database for all published Staphylococcus aureus transcriptional profiles.
  • To provide a platform for comprehensive analysis and comparison of S. aureus gene expression data.
  • To facilitate a deeper understanding of S. aureus pathogenesis mechanisms.

Main Methods:

  • Developed the Staphylococcus aureus Microarray meta-database (SAMMD) using MySQL and PHP/JavaScript/DHTML.
  • Collected data from peer-reviewed publications, employing Perl scripts for data extraction and phpMyAdmin for entry.
  • Implemented a web interface with features for searching, comparing datasets, browsing, downloading, and statistical analysis.

Main Results:

  • SAMMD is a relational database containing over 9,500 entries for regulated genes from 67 microarray experiments.
  • The database is accessible via a user-friendly web interface, supporting various analytical functions.
  • SAMMD is licensed under the General Public License (GPL).

Conclusions:

  • SAMMD provides a valuable resource for staphylococcal scientists to analyze and interpret gene expression data.
  • The meta-database enables global-level understanding of S. aureus gene regulation and pathogenesis.
  • It facilitates comparative transcriptomic analysis, allowing scientists to contrast their findings with published data.