Functional Genomics Data and Expression Look-up Tools: ArrayExpress and Expression Atlas

Expression Atlas at EMBL-EBI contains pre-analyzed RNA-seq and expression microarray data for researchers to discover and query which genes are expressed in which tissues, cell types, developmental stages, and many other experimental conditions.  Queries can either be in a baseline context, e.g. find genes expressed in the bovine kidney, or in a differential context, e.g. find genes that are up/downregulated in response to salt stress in rice. All datasets are manually curated to a high standard by our in-house curators and processed by our standardised statistical pipeline, both in consultation with experts around the world. As of October 2015, Expression Atlas consists of 2162 datasets, including 120 RNA-seq experiments. All data in Expression Atlas is free to browse, download, re-use, and is originated from the ArrayExpress archival database of functional genomics experiments at EMBL-EBI.

ArrayExpress experiments were either directly submitted by scientists working in diverse fields, or imported systematically from NCBI GEO weekly. As of October 2015, ArrayExpress consists of 60838 datasets (80% from microarrays) studying a wide variety of organisms, from cattle and chicken to barley and sorghum. Public ArrayExpress data sets are free for download, either from the website or programmatically.

Both databases employ EFO ontology-driven query expansion, enabling powerful searching across thousands of datasets.

Submission to ArrayExpress is a free service via a webform-based tool called Annotare.  To facilitate peer review, accession numbers are generated usually within 15 minutes of submission, pre-published data sets can be kept private, and submitter's identity can be hidden for double-blind review.