ArrayExpress—a public repository for microarray gene expression data at the EBI

ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from ∼12 000 hybridizations covering 35 species. Data can be submitted online or directly from local databases or LIMS in a standard format, and password-protected access to prepublication data is provided for reviewers and authors. The data can be retrieved by accession number or queried by vari-ous parameters such as species, author and array platform. A facility to query experiments by gene and sample properties is provided for a growing subset of curated data that is loaded in to the ArrayExpress data warehouse. Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress.

[1]  E. Birney,et al.  EnsMart: a generic system for fast and flexible access to biological data. , 2003, Genome research.

[2]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[3]  Graham Cameron,et al.  One-stop shop for microarray data , 2000, Nature.

[4]  C. Ball,et al.  Submission of Microarray Data to Public Repositories , 2004, PLoS biology.

[5]  Kazuho Ikeo,et al.  CIBEX: center for information biology gene expression database. , 2003, Comptes rendus biologies.

[6]  Alex Bateman,et al.  The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..

[7]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2004, Nucleic acids research.

[8]  David Botstein,et al.  The Stanford Microarray Database , 2001, Nucleic Acids Res..

[9]  Aedín C. Culhane,et al.  Expression Profiler: next generation - an online platform for analysis of microarray data , 2004, Nucleic Acids Res..

[10]  Martin Vingron,et al.  Microarray data representation, annotation and storage. , 2002, Advances in biochemical engineering/biotechnology.

[11]  Michael D Waters,et al.  Database development in toxicogenomics: issues and efforts. , 2004, Environmental health perspectives.

[12]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[13]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[14]  Jonathan Knight,et al.  Cancer comes under scrutiny in fresh genomics initiative , 2001, Nature.

[15]  Jason E. Stewart,et al.  Design and implementation of microarray gene expression markup language (MAGE-ML) , 2002, Genome Biology.

[16]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[17]  Syril D. Pettit,et al.  Use of Genomics in Mechanism Based Risk Assessment , 2003 .