Functional Genomics Resources: ArrayExpress and Expression Atlas

Date: Sunday, January 13, 2013
Time: 10:00 AM
Room: California
Gabriella Rustici , EMBL-EBI, Cambridge, United Kingdom
ArrayExpress is a public archive for well-annotated functional genomics data and has two major components:
  1. ArrayExpress Archive is a database of functional genomics data; it stores microarray and HTS data that are described and archived according to the community guidelines for microarray (MIAME) and HTS (MINSEQE) data;
  2. Expression Atlas is a database derived from data stored in the Archive, providing information about gene expression in different biological conditions

The Archive is built around experiments and can be used to retrieve actual data sets as well as information describing them. For example, you can access data files, sample annotations or assays relating to an experiment of interest. Data generated by microarray-based and HTS-based platforms can be submitted directly to the Archive. Some Archive data has been imported from the Gene Expression Omnibus, a public repository of functional genomics data at the NCBI, to provide users with a single access to most of the functional genomics data available in the public domain.

The Atlas' content derives from curation, re-annotation and statistical analysis of selected Archive data. The Atlas is built around genes and biological conditions and can be used to visualise changes in gene expression associated with different biological conditions, across different organisms.

The Archive and the Atlas are linked to other EBI databases such as ENA, Ensembl and Uniprot, which provide additional information on DNA and protein sequences and functions. Moreover, the two databases link out to data analysis software, such as Bioconductor and GenomeSpace, for the analysis of high-throughput data.