Functional Genomics Data and Expression look-up tools: ArrayExpress and new Expression Atlas

ArrayExpress is a public database for functional genomics data from microarray and sequencing studies, many supported by peer-reviewed publications. Common experiment types are expression profiling, SNP-typing and chromatin immunoprecipitation assays. Studies are submitted directly to ArrayExpress and manually curated, or imported from NCBI Gene Expression Omnibus weekly. Data are collected in conformity to the "Minimum Information About A Microarray/Seqeuncing Experiment" (MIAME/MINSEQE) standards. Users can search for studies of interest and download related information manually or programmatically, e.g. sample annotations, data files, protocols.

A subset of expression profiling experiments from ArrayExpress is reannotated and goes through a statistical analysis pipeline to generate the Expression Atlas, which consists of two components with slightly different focus: the "differential" and "baseline" atlases. Differential Atlas, containing both microarray and sequencing data, allows users to query which genes are up-/down-regulated in different experimental conditions (e.g. "In Arabidopsis shoots, what genes are upregulated in plants treated by X vs controls?"), or query by gene sets (e.g. genes in a Reactome pathway, genes matching a Gene Ontology term). The Baseline Atlas, containing exclusively RNA-seq data, displays expression levels of gene products under "normal" conditions (e.g. normal tissues from a rice plant).

The search functionalities in the above resources are powered by the Experimental Factor Ontology (www.ebi.ac.uk/efo), which expands your query where possible. E.g. searching for "rice" will match "Oryza sativa" as a synonym, while search term "bone" will also match "vertebra", "rib" as constituent ("child") terms.