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

Abstract

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/.

Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome

“…The microarray data for E. coli K-12 were downloaded from the M3D database (24) at http://m3d.bu.edu/. These data were collected under 380 experimental conditions and have been normalized across all the experiments so that the expressions of one gene can be compared directly across different experiments (24). The microarray data collected under 86 experimental conditions for B. subtilis str.…”

“…We have estimated the activation frequency of each pathway, based on the available microarray gene expression data. Specifically, we have used the microarray data for E. coli K-12 collected under 380 conditions from the M3D database (24), and the microarray data for B. subtilis str. 168 collected under 86 conditions from the KEGG database (17).…”

“…168 collected under 86 conditions from the KEGG database (17). All data are normalized across different experimental conditions so that the expression data for each gene collected under different conditions can be compared directly (24). We consider a pathway is activated if and only if at least X% of its operons are activated (different columns in Table 1), where an operon is considered activated if and only if its (average) expression value is higher than Y % of its expression values across all (available) conditions (different rows in Table 1), for parameters X and Y .…”

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

“…To this end, a large compendium composed of 445 microarray datasets was obtained from the M3D public database (Build 4 of E. coli expression data) [52]. These data were available in the form of Robust Multi Array (RMA) normalized profiles [53], which enables the direct comparison of the expression profiles of different protein-encoding genes across multiple experimental conditions.…”

Environmental Regulation of Prions in Yeast

“…Expression analysis of selected RNA-binders across conditions 247 microarray datasets (Affymetrix data) in the form of Robust Multi Array (RMA) normalized profiles were retrieved from the M3D database [26] (conditions are indicated in Table S3). Kmeans clustering was performed across conditions with the Euclidean distance metric and added into 10 groups.…”