Plant Gene Expression in EMBL-EBI Expression Atlas

Expression Atlas at EMBL-EBI (http://www.ebi.ac.uk/gxa) is a free online resource enabling users to discover which genes are expressed in which tissues, developmental stages, growth conditions, and hundreds of other experimental conditions across 19 different plant species (as well as others). This could either be in a baseline context, e.g. to find genes expressed in rice roots under normal conditions, or in a differential context, e.g. to find genes that are upregulated in response to drought stress in barley. The data in Atlas comes from the ArrayExpress archive of functional genomics experiments (http://www.ebi.ac.uk/arrayexpress). All datasets are manually curated to a high standard by our curators, with terms annotated using the Plant Ontology and the Experimental Factor Ontology. They are analysed with our in-house pipeline, using the latest microarray and RNA-seq analysis methods and following standard protocols. Differential expression comparisons are decided by curators, after assessment of the data, reading associated publications, and correspondence with the original researchers. The Expression Atlas website employs ontology-based query expansion to enable powerful searching across all the data. Newly available features include the ability to find genes with similar expression patterns, a new format for heatmaps displaying expression levels, and a Bioconductor package for searching and downloading data in R. The Gene Expression team have also recently released the RNA-seq Analysis API (http://www.ebi.ac.uk/fg/rnaseq/api/), providing processed RNA-seq data from millions of publicly available sequencing runs.