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

H Parkinson1, M Kapushesky, M Shojatalab

  • 1European Bioinformatics Institute, EMBL-EBI Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Nucleic Acids Research
|November 30, 2006
PubMed
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ArrayExpress is a public database for functional genomics data, archiving microarray experiments and providing gene expression profiles. It supports standards like MIAME and MAGE-TAB for data sharing.

Area of Science:

  • Functional Genomics
  • Bioinformatics
  • Data Archiving

Background:

  • ArrayExpress is a public database for high-throughput functional genomics data.
  • It comprises the ArrayExpress Repository for MIAME-supportive microarray data archiving and the ArrayExpress Data Warehouse for curated gene expression profiles.

Purpose of the Study:

  • To describe the structure and content of the ArrayExpress database.
  • To highlight its capabilities for querying and visualizing functional genomics data.
  • To emphasize its support for community data standards.

Main Methods:

  • Archiving of microarray hybridization data.
  • Re-annotation of gene expression profiles.
  • Development of query interfaces for experiment attributes and gene properties.

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  • Implementation of data visualization tools.
  • Support for community standards such as MIAME, MAGE-ML, and MAGE-TAB.

    • Main Results:

    • ArrayExpress contains over 50,000 hybridizations and 1,500,000 individual expression profiles.
    • The database allows querying by various experimental attributes (keywords, species, platform, authors, journals, accession numbers) and gene properties (Gene Ontology terms).
    • Data visualization of gene expression profiles is supported.

    Conclusions:

    • ArrayExpress serves as a comprehensive public resource for functional genomics data.
    • Its continuous growth and support for data standards facilitate data sharing and analysis within the research community.