Data repository · Database
ArrayExpress
A repository of functional genomics experiments, including microarray and sequencing studies, hosted by EMBL-EBI.
What ArrayExpress is
ArrayExpress is a public archive of high-throughput functional genomics experiments managed by the European Bioinformatics Institute (EMBL-EBI) and served via BioStudies. It provides biological researchers with access to experiment-level data for independent re-analysis and synthesis across studies.
The repository stores records spanning both microarray platforms and high-throughput sequencing technologies. By serving as an archive for primary functional genomics assays, it allows investigators to find, inspect, and retrieve raw and processed data alongside accompanying experimental context.
Studies curated in ArrayExpress are structured in accordance with community reporting guidelines. Each dataset includes comprehensive experimental metadata, protocols, sample descriptions, and links to underlying sequencing data.
How it is organised
Data submissions are managed through Annotare, a dedicated web-based deposition tool designed to collect experimental metadata, sample annotations, and protocols. Annotations and search queries are structured using the Experimental Factor Ontology to ensure consistent categorisation of biological conditions and factors.
Experiments in the database typically contain sample annotations, laboratory protocols, processed measurement files, and raw data files. When high-throughput sequencing assays are deposited, raw sequence reads are brokered to the European Nucleotide Archive (ENA), while ArrayExpress retains the experimental metadata and processed results alongside direct download links to the ENA sequence reads.
Key facts
- Category
- Functional genomics repository
- Platform types
- Microarray and high-throughput sequencing
- Deposition tool
- Annotare
- Data access methods
- Web interface, BioStudies, FTP, Aspera, ArrayExpress Bioconductor R package
- Ontology integration
- Experimental Factor Ontology (EFO)
- Sequence read archive
- European Nucleotide Archive (ENA)
What you can use it for
- Retrieving functional genomics datasets
- Researchers can search and download raw and processed data from historical microarray and sequencing studies for meta-analyses or re-evaluation.
- Programmatic analysis in R
- Bioinformaticians can use the ArrayExpress Bioconductor package to query experiments directly and load study records into R data structures.
- Archiving experiment data for publication
- Authors submitting functional genomics studies can deposit protocols, sample annotations, and data files via the Annotare web interface to comply with community standards.
Query it here
The research agent queries ArrayExpress directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Records adhere to community guidelines by linking protocols, detailed sample annotations, processed data, and raw files.
- The collection integrates with the Experimental Factor Ontology to support standardised querying and metadata annotation.
- Multiple programmatic and bulk transfer options are supported, including an R Bioconductor package, FTP, and Aspera.
Watch out for
- Raw sequencing reads are not hosted directly within the repository itself but are brokered to and retrieved from the European Nucleotide Archive.
- Depositions are restricted to functional genomics assays rather than broader biological data types.
Questions
Can I search ArrayExpress without writing code?
Yes. The research agent queries ArrayExpress directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from ArrayExpress?
EMBL-EBI Terms of Use; data as deposited by submitters. Cite the experiment accession (E-MTAB-…) and the publication that produced it. Terms: https://www.ebi.ac.uk/about/terms-of-use/
What types of experiments are included in ArrayExpress?
ArrayExpress holds high-throughput functional genomics experiments, specifically studies using microarray and high-throughput sequencing platforms.
How are raw sequence reads retrieved?
Raw sequence reads from sequencing studies are brokered to the European Nucleotide Archive (ENA), and ArrayExpress provides links to download the reads directly from ENA.
How can data be downloaded programmatically?
Data can be accessed and structured in R using the dedicated ArrayExpress Bioconductor package, or transferred in bulk via FTP and Aspera.
How are new experiments submitted to the repository?
Depositors use Annotare, a web-based submission tool that guides the provision of required experimental metadata, sample annotations, and data files.
Written from ArrayExpress's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.