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

Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

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/.

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All of the available E. coli Affymetrix Antisense2 expression data for the transcription factor lexA and its known target recA were downloaded from NCBI GEO Profiles (A) and from M3D compendium E_coli_v3_Build_1 (B and C). NCBI GEO Profile data is derived from NCBI GEO DataSets that contain only a subset of the data in GEO, therefore many more samples were available for plotting from M3D (445) than from GEO (85). The correlation between lexA and its known target was higher when the raw data was uniformly normalized with RMA (C) rather than normalizing each microarray individually with MAS5 (A and B).
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Figure 1: All of the available E. coli Affymetrix Antisense2 expression data for the transcription factor lexA and its known target recA were downloaded from NCBI GEO Profiles (A) and from M3D compendium E_coli_v3_Build_1 (B and C). NCBI GEO Profile data is derived from NCBI GEO DataSets that contain only a subset of the data in GEO, therefore many more samples were available for plotting from M3D (445) than from GEO (85). The correlation between lexA and its known target was higher when the raw data was uniformly normalized with RMA (C) rather than normalizing each microarray individually with MAS5 (A and B).

Mentions: Large microarray depositories like GEO and ArrayExpress focus on the archiving of expression data as used in specific publications. These archives play an essential role in biological science by allowing transparent replication of microarray analyses by other researchers. Experimenters using the same array platform often use different normalization methods for their analyses, so that data downloaded from different projects on GEO or ArrayExpress are unlikely to be directly comparable. GEO at NCBI provides GEO DataSets to alleviate this problem. A GEO DataSet contains a collection of biologically and statistically comparable microarray samples processed using the same platform. Unfortunately, there is a significant delay between when a sample is submitted to GEO and when it is available as a GEO DataSet. Only one-fifth of the number of samples in M3D were available from GEO DataSets (Figure 1A and B).Figure 1.


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

Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS - Nucleic Acids Res. (2007)

All of the available E. coli Affymetrix Antisense2 expression data for the transcription factor lexA and its known target recA were downloaded from NCBI GEO Profiles (A) and from M3D compendium E_coli_v3_Build_1 (B and C). NCBI GEO Profile data is derived from NCBI GEO DataSets that contain only a subset of the data in GEO, therefore many more samples were available for plotting from M3D (445) than from GEO (85). The correlation between lexA and its known target was higher when the raw data was uniformly normalized with RMA (C) rather than normalizing each microarray individually with MAS5 (A and B).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238822&req=5

Figure 1: All of the available E. coli Affymetrix Antisense2 expression data for the transcription factor lexA and its known target recA were downloaded from NCBI GEO Profiles (A) and from M3D compendium E_coli_v3_Build_1 (B and C). NCBI GEO Profile data is derived from NCBI GEO DataSets that contain only a subset of the data in GEO, therefore many more samples were available for plotting from M3D (445) than from GEO (85). The correlation between lexA and its known target was higher when the raw data was uniformly normalized with RMA (C) rather than normalizing each microarray individually with MAS5 (A and B).
Mentions: Large microarray depositories like GEO and ArrayExpress focus on the archiving of expression data as used in specific publications. These archives play an essential role in biological science by allowing transparent replication of microarray analyses by other researchers. Experimenters using the same array platform often use different normalization methods for their analyses, so that data downloaded from different projects on GEO or ArrayExpress are unlikely to be directly comparable. GEO at NCBI provides GEO DataSets to alleviate this problem. A GEO DataSet contains a collection of biologically and statistically comparable microarray samples processed using the same platform. Unfortunately, there is a significant delay between when a sample is submitted to GEO and when it is available as a GEO DataSet. Only one-fifth of the number of samples in M3D were available from GEO DataSets (Figure 1A and B).Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

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/.

Show MeSH
Related in: MedlinePlus