ArrayExpress

The ArrayExpress data collection in BioStudies (3) is a database of functional genomics data. It stores microarray and sequencing data that are described and archived according to the community guidelines for microarray (MIAME) and sequencing experiments (MINSEQE).

The focus of the database is on individual experiments and it can be used to retrieve actual experiments as well as the information describing them. Very often, one experiment corresponds to one publication in a journal. In the ArrayExpress data collection, you can access the raw data files, sample annotations or assays relating to an experiment of interest.

You can use ArrayExpress data to:

• Search by keywords or experiment’s properties (e.g. citation, transcriptomics platform, species or sample annotation) and identify experiments of interest;
• Download data associated with experiment(s), alongside its annotation, for your own analysis;
• Submit microarray or sequencing data that you want to publish. 

This image shows an example of search results from the ArrayExpress data collection in BioStudes. Click on to explore the results.

Figure 3 Example search results for the ArrayExpress data collection in BioStudies.

Submitting to ArrayExpress

The ArrayExpress collection has a dedicated submission tool, called Annotare. It is a user-friendly web tool that makes it easy for anyone to deposit their data. The submission forms in Annotare guide the submitter through the required metadata fields, in order to comply with the community standards for functional genomics: MIAME for microarray data; MINSEQE for high-throughput sequencing data; MINSCE for single-cell sequencing data. 

After submission, all datasets get checked by expert scientific curators. Once loaded into the database, an ArrayExpress study may remain in private status until its results are published or it is released by the submitter.

Learn more about ArrayExpress in the ArrayExpress in BioStudies: Quick tour.