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Related Concept Videos

DNA Microarrays02:34

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Performing Custom MicroRNA Microarray Experiments
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Published on: October 28, 2011

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata.

Jeremiah J Faith1, Michael E Driscoll, Vincent A Fusaro

  • 1Program in Bioinformatics, Boston University, 24 Cummington St. and Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, Massachusetts, 02215, USA.

Nucleic Acids Research
|October 13, 2007
PubMed
Summary

The Many Microbe Microarrays Database (M3D) offers normalized microbial expression data for Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis. This resource enables accessible data analysis and visualization for researchers studying microbial gene expression.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Systems Biology

Background:

  • Microbial expression data is often generated across multiple labs, leading to comparability challenges.
  • Analyzing large-scale microbial datasets requires standardized and accessible resources.
  • Existing databases may lack comprehensive, uniformly normalized data for key microbial species.

Purpose of the Study:

  • To establish a centralized database (M3D) for microbial expression data analysis.
  • To provide uniformly normalized microarray data for key model organisms.
  • To facilitate computational analysis and visualization of microbial gene expression.

Main Methods:

  • Compiled and uniformly normalized over a thousand Affymetrix microarrays for Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis.
  • Developed a database (M3D) with human-curated experimental metadata, including structured experimental features.
  • Implemented web-based tools for custom dataset construction, visualization, and download.

Main Results:

  • M3D hosts a substantial compendium of normalized microbial expression data.
  • Raw and normalized data are available for download, supporting computational analyses.
  • Web-based tools allow for efficient interrogation and custom dataset creation.

Conclusions:

  • M3D provides a valuable, accessible resource for microbial gene expression research.
  • Uniform normalization and curated metadata enhance data comparability and usability.
  • The database supports focused analyses and facilitates future interpretation of microbial expression studies.