ArrayExpress – functional genomics data

ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.

Latest News

26 February 2022 - ArrayExpress collection now released in BioStudies

The transition phase has begun! The ArrayExpress collection is now live in BioStudies. Head over to BioStudies and explore the new look of the archive, study pages, search filters and download functionality.

Here is an example: Current: E-MTAB-7871 New: E-MTAB-7871
Note that not all datasets have been migrated from ArrayExpress to BioStudies yet, so you may not find a particular experiment and search results will differ.

A quick summary of the changes to expect:

  • Programmatic data access will be available via the BioStudies API
  • Data download from FTP archives will change to BioStudies paths and functionality (e.g. adding Aspera download)
  • Post-submission modifications will be managed via the BioStudies submission tool (this is not yet available during the transition phase!)
And what stays the same:
  • All accession numbers will remain valid, and web links will be redirected
  • Annotare will remain the submission tool for adding new data
  • Study search powered by ontology expansion

Read more in our latest publication: Sarkans U et al. (2021) From ArrayExpress to BioStudies. Nucleic Acids Research 49, D1502–D1506

Please send any comments or questions to arrayexpress@ebi.ac.uk

Links

Information about how to search ArrayExpress, understand search results, how to submit data and FAQ can be found in our Help section.

Find out more about the Functional Genomics group.

Tools and Access

Annotare: web-based submission tool for ArrayExpress.

ArrayExpress Bioconductor package: an R package to access ArrayExpress and build data structures.

Programmatic access: query and download data using web services or JSON.

FTP access: data can be downloaded directly from our FTP site.

Related Projects

Discover up and down regulated genes in numerous experimental conditions in the Expression Atlas.

Explore the Experimental Factor Ontology used to support queries and annotation of ArrayExpress data.