GEO (40) is a data repository and retrieval system for high-throughput functional genomic data generated by microarray and next-generation sequencing technologies. In addition to gene expression data, GEO accepts other categories of experiments including studies of genome copy number variation, genome–protein interaction surveys and methylation profiling studies. The repository can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as ‘Minimum Information about a Microarray Experiment’ (41,42). Several data deposit options and formats are supported, including web forms, spreadsheets, XML and plain text. GEO data are housed in two Entrez databases: GEO Profiles, which contains quantitative gene expression measurements for one gene across an experiment, and GEO data sets, which contain entire experiments. Currently, the GEO database hosts over 13 000 experiments submitted by 6500 laboratories and comprising 330 000 samples and 23 billion individual abundance measurements for over 700 organisms.
