Functional Genomics Resources at EBI: ArrayExpress and Expression Atlas

Expression Atlas consists of pre-analyzed RNA-seq and expression microarray data, to enable users to discover which genes are expressed in which tissues, cell types, developmental stages, and hundreds of other experimental conditions. This could be either in a baseline context, e.g. to find genes expressed in the bovine kidney, or in a differential context, e.g. to find genes that are upregulated in response to salt stress in rice. All datasets are manually curated to a high standard, by our in-house curators and using advice from experts around the world. At the time of writing, Expression Atlas consists of 802 datasets, including 47 RNA-seq experiments. All data in Expression Atlas is free to browse, download, and re-use. ArrayExpress is an archive of functional genomics experiments, submitted by scientists working in diverse fields. Submission to ArrayExpress is free of charge, and datasets can be kept private until the submitter publishes their findings. Submission is now quicker and easier than ever before, thanks to our new tool, Annotare: most submissions are accessioned within 24 hours. ArrayExpress also imports all new releases from NCBI GEO weekly.  As of October 2014, ArrayExpress consists of 53782 datasets studying a wide variety of organisms, from cattle and chicken to rice and maize. The majority of ArrayExpress data is microarray based, though our RNA-seq coverage is growing daily. Public data in ArrayExpress is freely available for download, either from the website or via programmatic access. Both resources employ ontology-driven query expansion, enabling powerful searching across thousands of datasets.