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Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2008 36(Database issue):D866-D870; doi:10.1093/nar/gkm815
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Nucleic Acids Research, 2008, Vol. 36, Database issue D866-D870
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

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

Jeremiah J. Faith1, Michael E. Driscoll1, Vincent A. Fusaro1, Elissa J. Cosgrove2, Boris Hayete1, Frank S. Juhn2, Stephen J. Schneider2 and Timothy S. Gardner1,2,*

1Program in Bioinformatics, Boston University, 24 Cummington St. and 2Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, Massachusetts, 02215, USA

* To whom correspondence should be addressed. Tel: +617 358 0745; Fax: +617 358 0744; Email: tgardner{at}bu.edu

Received August 15, 2007. Revised September 17, 2007. Accepted September 18, 2007.

Many Microbe Microarrays Database (M3D) is designed to facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories. M3D contains over a thousand Affymetrix microarrays for Escherichia coli, Saccharomyces cerevisiae and Shewanella oneidensis. The expression data is uniformly normalized to make the data generated by different laboratories and researchers more comparable. To facilitate computational analyses, M3D provides raw data (CEL file) and normalized data downloads of each compendium. In addition, web-based construction, visualization and download of custom datasets are provided to facilitate efficient interrogation of the compendium for more focused analyses. The experimental condition metadata in M3D is human curated with each chemical and growth attribute stored as a structured and computable set of experimental features with consistent naming conventions and units. All versions of the normalized compendia constructed for each species are maintained and accessible in perpetuity to facilitate the future interpretation and comparison of results published on M3D data. M3D is accessible at http://m3d.bu.edu/.


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