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

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Abstract
Many Microbe Microarrays Database (M 3D ) is designed to facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories. M 3D 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, M 3D 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 M 3D 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 M 3D data. M 3D is accessible at http://m3d.bu.edu/ .