Expression Atlas - a New Resource for Baseline and Differential Gene Expression for Crop Plants

Expression Atlas (http://www.ebi.ac.uk/gxa) consists of RNA-seq and microarray experiments, selected and manually curated from the ArrayExpress functional genomics repository.  The data in Atlas has been pre-analysed and quality controlled using standardised in-house processing pipelines, against the latest genome references in Ensembl Plants. Users are able to search Atlas for information about which genes are expressed in which tissues, cell types, developmental stages, and many other experimental conditions. This information can be in a baseline context, e.g. to find out which genes are expressed in the Arabidopsis thaliana Sf-2 strain, or in a differential context, e.g. to find genes that are upregulated in response to salt stress in rice. All datasets are annotated to Experimental Factor Ontology (EFO), and Plant Ontology where possible. At the time of writing, Expression Atlas contains 220 Arabidposis and 9 rice data sets (including 3 experiments studying baseline expression in tissues and strains). Our first maize data sets are also currently being curated and analysed. Users are able to view expression data in Ensembl Plants and Gramene Genome browsers.  Atlas also offers gene set overlap analysis (Fisher-exact) for Reactome Pathways, GO terms, and soon for Plant Reactome pathways.  Finally, thanks to our new submissions tool called Annotare (http://www.ebi.ac.uk/fgpt/annotare_help/), most submissions to ArrayExpress are completed within one day, and all the relevant experimental data is captured and where possible mapped to EFO. We plan to adapt the tool to make richly annotated plant experiment submissions easier for our submitters.