Abstract
ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter occupancy. The number of experiments based on sequencing technologies, in particular RNA-seq experiments, has been increasing over the last few years and submissions of sequencing data have overtaken microarray experiments in the last 12 months. Additionally, there is a significant increase in experiments investigating single cells, rather than bulk samples, known as single-cell RNA-seq. To accommodate these trends, we have substantially changed our submission tool Annotare which, along with raw and processed data, collects all metadata necessary to interpret these experiments. Selected datasets are re-processed and loaded into our sister resource, the value-added Expression Atlas (and its component Single Cell Expression Atlas), which not only enables users to interpret the data easily but also serves as a test for data quality. With an increasing number of studies that combine different assay modalities (multi-omics experiments), a new more general archival resource the BioStudies Database has been developed, which will eventually supersede ArrayExpress. Data submissions will continue unchanged; all existing ArrayExpress data will be incorporated into BioStudies and the existing accession numbers and application programming interfaces will be maintained.
Highlights
ArrayExpress is an archive of functional genomics data that includes a range of experiment types, such as gene expression, methylation profiling and chromatin immunoprecipitation assays
ArrayExpress was first established as a database for microarray data in 2002 [1] and for the last decade has been one of the core archival resources at the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
The raw sequences are stored in the European Nucleotide Archive (ENA), whilst ArrayExpress retains any processed data, such as gene expression matrices, experimental metadata, e.g. what experimental variables have been tested in the experiment, as well as other metadata necessary for data re-use
Summary
ArrayExpress is an archive of functional genomics data that includes a range of experiment types, such as gene expression, methylation profiling and chromatin immunoprecipitation assays. ArrayExpress accepts submissions via the webtool Annotare and is the main source of data for the Expression Atlas [2] – a value-added gene expression database at EMBL-EBI, which allows for gene-, tissue- or disease-based queries.
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