Functional genomic resources at the EBI
This section will introduce you to the functional genomic resources at the EBI:
- ArrayExpress 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;
- Gene Expression Atlas (the ‘Atlas’) is a database derived from data stored in ArrayExpress, providing information about gene expression in different biological conditions (for example: different cell types, organism parts and disease states).
ArrayExpress is built around experiments and can be used to retrieve actual experiments 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 ArrayExpress using one of the following tools: MIAMExpress and MAGE-TAB (5). Submitting data to ArrayExpress allows the scientific community to perform searches and analysis on the latest functional genomics data. Some ArrayExpress data has been imported from the Gene Expression Omnibus (GEO), a public repository of functional genomics data at the NCBI, to expand the number of studies that are available in ArrayExpress.
The Atlas derives from curation, re-annotation and statistical analysis of selected ArrayExpress data (4) (Figure 1.2). 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.
ArrayExpress and the Atlas are linked to other EBI databases such as ENA, Ensembl, 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 (6), a tool for the analysis and comprehension of high-throughput genomic data.
Figure 1.2. Selected data from ArrayExpress are re-annotated and analysed statistically before being placed in the Atlas database.