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

TLDR

ArrayExpress is one of three major international functional genomics public data repositories, alongside GEO and the DDBJ Omics Archive, supporting peer‑reviewed publications. It stores nearly a million assays from over 30 000 experiments generated by sequencing or array technologies, provides data in MAGE‑TAB format for linkage to analysis tools such as Bioconductor and GenomeSpace, and supplies R objects for microarray data and BAM files for sequencing data. Sequencing‑based submissions now account for 15 % of all new data in 2012, a significant increase over the previous two years.

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.