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M3D (Many Microbe Microarrays) was developed by the Gardner Lab at Boston University to facilitate the exchange and analysis of high quality, curated, microbial gene expression data. Currently, the database only includes data obtained using Affymetrix GeneChip technology, because the high quality of the platform facilitates cross-laboratory integration of data sets.
The database allows downloading of raw data (CEL files) or preprocessed data that has been uniformly normalized with RMA.
M3D also enables convenient web-based expression data exploration and visualization - accessable via the Analysis page.
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| Citing M3D |
| Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, and Gardner TS. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Research |
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| Data Contributors |
| The data in M3D was compiled from multiple laboratories.
Each project in the database (viewable in the Analysis section) has links to the relevant publications. |
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| Acknowledgements |
| The following free software and libraries were used for array normalization and to develop this site: dChip, Bioconductor (for RMA), gd,
cgic,
Cluster 3.0, libwebplot,
lightweight genome viewer, and
MySQL.
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| Database developed by |
| Jeremiah Faith, Mike Driscoll, Frank Juhn, Stephen Schneider, Elissa Cosgrove, and Boris Hayete in the Department of Biomedical Engineering and Program in Bioinformatics at Boston University. |
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| Website developed by |
| Jeremiah Faith and Vincent Fusaro |
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