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A comparative account of gene expression resources, feature-validations and application-based categorizations

ArrayExpress

Tool nameArrayExpress
URLhttp://www.ebi.ac.uk/arrayexpress
Important featuresA database of functional genomics experiments with MIAME and MINSEQE standards. The data can be queried and downloaded. Gene Expression Atlas contains a subset of curated and re-annotated archive data, which can be queried for individual gene expression under different biological conditions across experiments.
CitationsBrazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003 Jan 1;31(1):68-71. PubMed PMID: 12519949; PubMed Central PMCID: PMC165538.
Year of publication2003
Rank by usage frequency100
Comments
FunctionMicroarray, Other technique(s), Multiple techniques, Human, Mouse, Rat, Plant, Other species, Multiple species, Raw data repository
CategoryOnline, Free
Working statusFunctional
Other features
Other citations1. Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA. ArrayExpress: a public database of gene expression data at EBI. C R Biol. 2003 Oct-Nov;326(10-11):1075-8. PubMed PMID: 14744115. 2. Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D553-5. PubMed PMID: 15608260; PubMed Central PMCID: PMC540010. 3. Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A. ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 2007 Jan;35(Database issue):D747-50. Epub 2006 Nov 28. PubMed PMID: 17132828; PubMed Central PMCID: PMC1716725. 4. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. Epub 2008 Nov 10. PubMed PMID: 19015125; PubMed Central PMCID: PMC2686529. 5. Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A. ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4. Epub 2010 Nov 10. PubMed PMID: 21071405; PubMed Central PMCID: PMC3013660.

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