ArrayExpress update--trends in database growth and links to data analysis tools

Abstract

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

Figure 1.

Sample–data relationship viewer for Experiment E-MTAB-513. This view provides information on sample characteristics and experimental variables that are fundamental to understand the results obtained in the experiment. Generally, each row corresponds to a sample. Columns include sample characteristics and their relationship to the resulting data files, providing a quick view over the structure of the experiment and the biological questions that the authors addressed. The last column provides links to raw sequence data files available in ENA, and BAM files that can be visualized in the Ensembl genome browser.