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Data storage and analysis in ArrayExpress.

Alvis Brazma1, Misha Kapushesky, Helen Parkinson

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Methods in Enzymology
|August 31, 2006
PubMed
Summary
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ArrayExpress is a public database archiving and analyzing gene expression profiles from over 1200 studies. It provides tools for data submission, retrieval, and analysis, supporting scientific publications.

Area of Science:

  • Bioinformatics
  • Genomics
  • Data Archiving

Background:

  • ArrayExpress serves as a public resource for microarray data.
  • It aims to archive data supporting publications and build a gene expression knowledge base.

Purpose of the Study:

  • To describe the ArrayExpress components for users.
  • To guide users on data submission, retrieval, and analysis.

Main Methods:

  • ArrayExpress integrates a repository (archive) and a data warehouse (reannotated, query-optimized).
  • Includes tools like Expression Profiler (EP) for data mining and MIAMExpress for submission.

Main Results:

  • As of December 2005, it contained data from ~35,000 hybridizations across 1200+ studies and 70 species.

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  • Data is queryable by various parameters, enabling combined data retrieval from different studies.

    • Conclusions:

    • ArrayExpress is a comprehensive resource for managing and analyzing public microarray data.
    • It facilitates access to gene expression profiles and supports the scientific community.