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

1 October 2020 - ArrayExpress is moving to BioStudies
The European Bioinformatics Institute (EMBL-EBI) is building and maintaining the BioStudies Database, a resource for encapsulating all the data associated with a biological study. One of the goals of BioStudies is to accept and archive data generated in experiments that can be characterized as "multi-omics". To streamline the data management systems and data representation at EMBL-EBI, we will start hosting data currently served from ArrayExpress in BioStudies under the ArrayExpress collection. This process will be largely seamless for our data submitters and users:

  1. The submissions of gene expression and related functional genomics data (including methylation profiling and ChIP-seq data) will continue to be handled by the Annotare submission tool.
  2. All data in ArrayExpress are being transferred to BioStudies, and the accession numbers will be maintained.
  3. The current links to experiments in ArrayExpress will remain valid (and will be redirected to BioStudies).
  4. All current ArrayExpress query functionality will be conserved in BioStudies, and access to MAGE-TAB files will be provided both for the existing ArrayExpress experiments and the future submissions via Annotare.
However, some changes will happen, in particular:
  1. There will be differences in how experiments are presented in the web interface, in particular, the "samples" view.
  2. The existing API functionality will be available from BioStudies, but changes will be necessary (preview the migration guide).
  3. Submitters will manage post-submission modifications (such as release date changes) via the BioStudies submission tool.
There are two phases of migration that are relevant to ArrayExpress users. During the first phase all new experiments will be made available in both the current ArrayExpress interface and the “beta” instance of BioStudies, and we will be looking for feedback from submitters and users on data representation in BioStudies and usability. Data submitters will receive a link to their data in BioStudies in the confirmation e-mail that is sent upon successful loading of a submission. This phase will start in October 2020. Once we have incorporated the user feedback into our pipelines and made sure that all processes work smoothly, we will retire the current ArrayExpress infrastructure, aiming for Spring 2021.

We would like to thank all ArrayExpress users and submitters for their patience while we carry out this work. 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.