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

Faith, J. J.; Driscoll, M. E.; Fusaro, V. A.; Cosgrove, E. J.; Hayete, B.; Juhn, F. S.; Schneider, S. J.; Gardner, T. S.

doi:10.1093/nar/gkm815

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

Journal Article · Thu Oct 11 00:00:00 EDT 2007 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkm815· OSTI ID:1625431

Faith, J. J. ^[1]; Driscoll, M. E. ^[2]; Fusaro, V. A. ^[2]; Cosgrove, E. J. ^[3]; Hayete, B. ^[2]; Juhn, F. S. ^[3]; Schneider, S. J. ^[3]; Gardner, T. S. ^[4]

Boston Univ., MA (United States). Program in Bioinformatics; DOE/OSTI
Boston Univ., MA (United States). Program in Bioinformatics
Boston Univ., MA (United States). Dept. of Biomedical Engineering
Boston Univ., MA (United States). Program in Bioinformatics; Boston Univ., MA (United States). Dept. of Biomedical Engineering

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. M3D is accessible at http:// m3d.bu.edu/.

View Accepted Manuscript (DOE)

Research Organization:: Boston Univ., MA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: FG02-04ER63803; FG02-07ER64388

OSTI ID:: 1625431

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: suppl_1 Vol. 36; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (18)

Reverse-engineering transcription control networks Gardner, T.; Faith, J. Physics of Life Reviews, Vol. 2, Issue 1 https://doi.org/10.1016/j.plrev.2005.01.001	journal	March 2005
Functional Discovery via a Compendium of Expression Profiles Hughes, Timothy R.; Marton, Matthew J.; Jones, Allan R. Cell, Vol. 102, Issue 1 https://doi.org/10.1016/s0092-8674(00)00015-5	journal	July 2000
Predicting Gene Expression from Sequence Beer, Michael A.; Tavazoie, Saeed Cell, Vol. 117, Issue 2 https://doi.org/10.1016/s0092-8674(04)00304-6	journal	April 2004
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks di Bernardo, Diego; Thompson, Michael J.; Gardner, Timothy S. Nature Biotechnology, Vol. 23, Issue 3 https://doi.org/10.1038/nbt1075	journal	March 2005
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data Brazma, Alvis; Hingamp, Pascal; Quackenbush, John Nature Genetics, Vol. 29, Issue 4 https://doi.org/10.1038/ng1201-365	journal	December 2001
Reverse engineering of regulatory networks in human B cells Basso, Katia; Margolin, Adam A.; Stolovitzky, Gustavo Nature Genetics, Vol. 37, Issue 4 https://doi.org/10.1038/ng1532	journal	March 2005
Network component analysis: Reconstruction of regulatory signals in biological systems Liao, J. C.; Boscolo, R.; Yang, Y. -L. Proceedings of the National Academy of Sciences, Vol. 100, Issue 26 https://doi.org/10.1073/pnas.2136632100	journal	December 2003
ASAP, a systematic annotation package for community analysis of genomes Glasner, J. D. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg125	journal	January 2003
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Salgado, H. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj156	journal	January 2006
NCBI GEO: mining tens of millions of expression profiles--database and tools update Barrett, T.; Troup, D. B.; Wilhite, S. E. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl887	journal	January 2007
Entrez Gene: gene-centered information at NCBI Maglott, D.; Ostell, J.; Pruitt, K. D. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl993	journal	January 2007
ArrayExpress--a public database of microarray experiments and gene expression profiles Parkinson, H.; Kapushesky, M.; Shojatalab, M. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl995	journal	January 2007
Summaries of Affymetrix GeneChip probe level data Irizarry, R. A. Nucleic Acids Research, Vol. 31, Issue 4 https://doi.org/10.1093/nar/gng015	journal	February 2003
Lightweight Genome Viewer: portable software for browsing genomics data in its chromosomal context Faith, Jeremiah J.; Olson, Andrew J.; Gardner, Timothy S. BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-344	journal	January 2007
Functional Discovery via a Compendium of Expression Profiles Hughes, Timothy R.; Marton, Matthew J.; Jones, Allan R. Cell, Vol. 102, Issue 1 https://doi.org/10.1016/S0092-8674(00)00015-5	journal	July 2000
Predicting Gene Expression from Sequence Beer, Michael A.; Tavazoie, Saeed Cell, Vol. 117, Issue 2 https://doi.org/10.1016/S0092-8674(04)00304-6	journal	April 2004
EcoCyc: a comprehensive database resource for Escherichia coli Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro Nucleic Acids Research, Vol. 33, Issue suppl_1, p. D334-D337 https://doi.org/10.1093/nar/gki108	journal	December 2004
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles Faith, Jeremiah J.; Hayete, Boris; Thaden, Joshua T. PLoS Biology, Vol. 5, Issue 1 https://doi.org/10.1371/journal.pbio.0050008	journal	January 2007

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MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections Bentham, Robert B.; Bryson, Kevin; Szabadkai, Gyorgy https://doi.org/10.1101/075374	posted_content	September 2016
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Gene set analysis: limitations in popular existing methods and proposed improvements Mishra, Pashupati; Törönen, Petri; Leino, Yrjö Bioinformatics, Vol. 30, Issue 19 https://doi.org/10.1093/bioinformatics/btu374	journal	June 2014
CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data Feichtinger, Julia; McFarlane, Ramsay J.; Larcombe, Lee D. Database, Vol. 2012 https://doi.org/10.1093/database/bas055	journal	January 2012
Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis Beg, Qasim K.; Zampieri, Mattia; Klitgord, Niels Nucleic Acids Research, Vol. 40, Issue 15 https://doi.org/10.1093/nar/gks467	journal	May 2012
Distinct transcriptional regulation of the two Escherichia coli transhydrogenases PntAB and UdhA Haverkorn van Rijsewijk, Bart R. B.; Kochanowski, Karl; Heinemann, Matthias Microbiology, Vol. 162, Issue 9 https://doi.org/10.1099/mic.0.000346	journal	September 2016
Chaperonin Abundance Boosts Bacterial Fitness Kumar, C. M. Santosh; Chugh, Kritika; Dutta, Anirban BioRxiv https://doi.org/10.1101/2019.12.31.891820	posted_content	January 2020
Predicting protein targets for drug-like compounds using transcriptomics Pabon, Nicolas A.; Xia, Yan; Estabrooks, Samuel K. BioRxiv https://doi.org/10.1101/254367	posted_content	January 2018
Inference of bacterial small RNA regulatory networks and integration with transcription factor driven regulatory networks Arrieta-Ortiz, Mario L.; Hafemeister, Christoph; Shuster, Bentley mSystems https://doi.org/10.1101/657478	journal	January 2019
Adversarial generation of gene expression data Viñas, Ramon; Andrés-Terré, Helena; Liò, Pietro https://doi.org/10.1101/836254	posted_content	January 2019
Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks Al Mamun, A. A. M.; Lombardo, M. -J.; Shee, C. Science, Vol. 338, Issue 6112 https://doi.org/10.1126/science.1226683	journal	December 2012
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection Haury, Anne-Claire; Mordelet, Fantine; Vera-Licona, Paola BMC Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1186/1752-0509-6-145	journal	January 2012
A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes Scherrer, Tanja; Mittal, Nitish; Janga, Sarath Chandra Investigations in Yeast Functional Genomics and Molecular Biology https://doi.org/10.1201/b16586-17	book	February 2014
Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data Treviño, Santiago; Sun, Yudong; Cooper, Tim F. PLoS Computational Biology, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pcbi.1002391	journal	February 2012
A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes Scherrer, Tanja; Mittal, Nitish; Janga, Sarath Chandra PLoS ONE, Vol. 5, Issue 11 https://doi.org/10.1371/journal.pone.0015499	journal	November 2010
De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae Ma, Sisi; Kemmeren, Patrick; Gresham, David PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0106479	journal	September 2014
Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation Junier, Ivan; Rivoire, Olivier PLOS ONE, Vol. 11, Issue 5 https://doi.org/10.1371/journal.pone.0155740	journal	May 2016
Adversarial generation of gene expression data. Viñas Torné, Ramon; Andrés-Terré, Helena; Lio, Pietro Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.63503	text	January 2021
Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data Treviño, Santiago; Sun, Yudong; Cooper, Tim F. arXiv https://doi.org/10.48550/arxiv.1201.2366	text	January 2012
Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries Carlson, Michael Luke; Stacey, R. Greg; Young, John William eLife, Vol. 8 https://doi.org/10.7554/elife.46615	journal	July 2019

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