Many Microbe Microarrays Database (M3D)

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Many Microbe Microarrays Database

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Affymetrix data for E. coli and other bacteria


Tim Gardner

Boston University

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About Many Microbe Microarrays Database (M3D)

Home Page

Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.[1]


Experiments: 189 Arrays: 445

Using Many Microbe Microarrays Database (M3D)



Users can query M3D by choosing a project and a list of genes. Data can be normalized (scaling by gene) prior to analysis.

Presentation formats include:

  • Heat Plot (genes vs experiments)
  • Histogram of individual gene expression (one plot per gene)
  • Histogram of all gene expression (one plot for N genes)
  • Plot Expression of many genes as a function of one gene
  • Link to download expression data

Average Array Replicates by:

  • RMA
  • DchipPM
  • DchipMM
  • MAS5

Heat Plot Parameters:

  • rescale data to within stddev of mean
  • Order Genes By Correlation
  • Order Experiments By Correlation

Heat Map coloring:

  • Red/Blue
  • Red/Green

M3D provides a meatalink to execute queries on N-browse, which is described as an interactive graphical browser for molecular interaction networks

Usage examples

Add links to additional pages describing success stories here.

Other sites with related content


The following free software and libraries were used for array normalization and to develop M3D: dChip, Bioconductor (for GCRMA and RMA), gd, cgic, Cluster 3.0, and MySQL.

Web Services/API



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See Help:References for how to manage references in EcoliWiki.

  1. Faith, JJ et al. (2008) Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res. 36 D866-70 PubMed

External Links

Many Microbe Microarrays Database (M3D)

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