Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Jan;35(Database issue):D747-50.
doi: 10.1093/nar/gkl995. Epub 2006 Nov 28.

ArrayExpress--a public database of microarray experiments and gene expression profiles

H Parkinson  1 , M Kapushesky, M Shojatalab, N Abeygunawardena, R Coulson, A Farne, E Holloway, N Kolesnykov, P Lilja, M Lukk, R Mani, T Rayner, A Sharma, E William, U Sarkans, A Brazma
Affiliations

ArrayExpress--a public database of microarray experiments and gene expression profiles

H Parkinson et al. Nucleic Acids Res. 2007 Jan.

Abstract

ArrayExpress is a public database for high throughput functional genomics data. ArrayExpress consists of two parts--the ArrayExpress Repository, which is a MIAME supportive public archive of microarray data, and the ArrayExpress Data Warehouse, which is a database of gene expression profiles selected from the repository and consistently re-annotated. Archived experiments can be queried by experiment attributes, such as keywords, species, array platform, authors, journals or accession numbers. Gene expression profiles can be queried by gene names and properties, such as Gene Ontology terms and gene expression profiles can be visualized. ArrayExpress is a rapidly growing database, currently it contains data from >50,000 hybridizations and >1,500,000 individual expression profiles. ArrayExpress supports community standards, including MIAME, MAGE-ML and more recently the proposal for a spreadsheet based data exchange format: MAGE-TAB.

Availability: www.ebi.ac.uk/arrayexpress.

PubMed Disclaimer

Figures

Figure 1
Figure 1
ArrayExpress experiment query form. Queries on experiment properties: organisms, author's names, array types or accession numbers are supported.
Figure 2
Figure 2
A detailed view of an experiment from the repository. Strings matching the query terms are highlighted in yellow.
Figure 3
Figure 3
Gene expression profiles query form. Queries on gene properties: names, accession numbers, synonyms and gene ontology terms are supported.
Figure 4
Figure 4
A view of gene expression for gene ‘aspm’ within a single experiment in the data warehouse.
See this image and copyright information in PMC

References

    1. Parkinson H., Sarkans U., Shojatalab M., Abeygunawardena N., Contrino S., Coulson R., Farne A., Lara G.G., Holloway E., Kapushesky M., et al. ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2005;33:D553–D555. - PMC - PubMed
    1. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genet. 2001;29:365–371. - PubMed
    1. Ball C.A., Brazma A., Causton H., Chervitz S., Edgar R., Hingamp P., Matese J.C., Parkinson H.E., Quackenbush J., Ringwald M., et al. Submission of microarray data to public repositories. PLoS Biol. 2004;2:E317. - PMC - PubMed
    1. Edgar R., Domrachev M., Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207–210. - PMC - PubMed
    1. Ikeo K., Ishi-I J., Tamura T., Gojobori T., Tateno Y. CIBEX: center for information biology gene expression database. C. R. Biol. 2003;326:1079–1082. - PubMed

Publication types