Summary

• Functional genomics attempts to understand the complex relationship between genotype and phenotype on a global scale using high-throughput technologies, such as microarrays and high-throughput sequencing
• The functional genomics resources at EMBL-EBI consist of the ArrayExpress collection in BioStudies, Expression Atlas and Single Cell Expression Atlas
• The ArrayExpress data collection in BioStudies is a collection of functional genomics data supported by scientific publications
• Expression Atlas is a database providing information about gene expression in different biological conditions (for example in different cell types, organisms parts, diseases, compound treatments and genotypes)
• Single Cell Expression Atlas is a database of single cell expression datasets
• The difference between the two databases is that ArrayExpress is built around experiments (containing information on data files, sample annotation and others), whereas the Atlas is built around genes and biological conditions and is used to visualise changes in gene expression associated with different biological conditions
  

Using an analogy of cooking, you can think of ArrayExpress as a place where you can source all raw cooking “ingredients” (raw data files with associated sample annotation), and you are free to go away and create your own dishes or make a meal out of them. If you do not fancy cooking, or don’t have the time/skills/tools to do so, Expression Atlas is like a “canteen” where pre-defined “dishes” (analysed gene expression data) are already prepared from the finest “ingredients” for your consumption.