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

24 November 2017 - Latest Annotare release is out – plant templates, suggested experimental variables and more!

We are proud to announce the latest release of our submission tool Annotare. The new version provides a number of new features aimed at improving metadata quality and speeding up the submission and curation process. Information about all the new features as well as how to use Annotare can be found in our updated Annotare help pages.
Our key feature is the development of new templates for plant submissions. These were developed in collaboration with plant scientists within the Gramene project, funded by the National Science Foundation (NSF). The plant templates provide tailored sample metadata fields and specifies plant-specific protocols required for understanding and reproducing plant experiments.
. In addition, we addressed the issue of finding the right experimental variable in all submissions. Depending on your experimental design, Annotare now pre-selects the appropriate experimental variable. For example, in experiments were compound effects are tested, Annotare now suggests providing information about the compound and dose used.
Lastly, we also took into account submitter feedback and provided extra help with both the template (microarray or sequencing) selection and file assignment for technical replicates, paired or single-end sequencing files.
We would like to thank submitters for their patience and for providing informative and useful feedback. We are always happy to hear from you! Enjoy submitting!

13 October 2017 - ArrayExpress is stopping import of GEO data

Unfortunately, we are stopping the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. We will keep using data from GEO to build our added value database Expression Atlas, and the reprocessed and additionally annotated data for selected datasets will be available from there.


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.