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ArrayExpress update--trends in database growth and links to data analysis tools.

Gabriella Rustici1, Nikolay Kolesnikov, Marco Brandizi

  • 1Functional Genomics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK. gabry@ebi.ac.uk

Nucleic Acids Research
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PubMed
Summary
This summary is machine-generated.

The ArrayExpress Archive stores functional genomics data from nearly a million assays. This public repository supports peer-reviewed publications and links data to analysis tools.

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Area of Science:

  • Functional Genomics
  • Bioinformatics
  • Data Archiving

Background:

  • ArrayExpress is a key international public repository for functional genomics data.
  • It complements other major repositories like Gene Expression Omnibus (GEO) and DDBJ.
  • Supports data from peer-reviewed publications, ensuring research integrity.

Purpose of the Study:

  • To describe the ArrayExpress Archive of Functional Genomics Data.
  • To highlight its role in supporting scientific publications and data accessibility.
  • To detail the types of data and formats available.

Main Methods:

  • Accepts data from both array-based and sequencing technologies.
  • Data are stored and made available in the MAGE-TAB format.
  • Generates R objects for microarray data and binary alignment files for sequencing data.

Main Results:

  • Contains data from over 30,000 experiments and nearly one million assays.
  • Shows a significant increase in sequencing-based submissions, reaching 15% in 2012.
  • Provides robust linking of data to analysis and visualization tools (e.g., Bioconductor, GenomeSpace).

Conclusions:

  • ArrayExpress is a vital resource for functional genomics research, offering comprehensive data archiving.
  • The increasing proportion of sequencing data reflects technological shifts in the field.
  • Standardized data formats and tool integration enhance data usability and reproducibility.