Summary

 

What is ArrayExpress?
ArrayExpress is a repository for functional genomics data sets, which are organised into experiments. An experiment consists of metadata, raw data files and processed data files. Both, microarray and sequencing (NGS) technology are supported.

Why use ArrayExpress?
ArrayExpress provides one access point for public functional genomic data sets. Many journals now require functional genomics data sets to be deposited at a public database like ArrayExpress to facilitate data sharing. ArrayExpress curators curate direct submissions according to community guidelines (MIAME or MINSEQE) to ensure data reproducibility.

How are experiments and data files stored in ArrayExpress?
Each experiment contains meta-data which is split into two parts: 1) IDF which describes the experiment and 2) SDRF which describes the sample attributes and how data files are linked to the samples. Many experiments contain raw (unprocessed) data files, and some contain processed (normalised) data matrices.

How can I find experiments in ArrayExpress?
You can retrieve experiment information and data files by searching the metadata fields. You can easily filter results by specifying e.g. species, technology type, or experimental variables.

How can I use (re-reuse) data from ArrayExpress?
The raw data files can be downloaded and processed using many open-source bioinformatics tools. Where available, analyses of normalised data can be done. It is fine to publish the results while citing the relevant ArrayExpress accession(s).