NCBI GEO: archive for functional genomics data sets--10 years on

TLDR

The Gene Expression Omnibus (GEO) was established ten years ago as a public repository for high‑throughput gene expression data, primarily from microarrays. This paper describes recent database enhancements, including new search and data representation tools, and reviews how the community uses GEO data. GEO’s flexible structure has allowed it to evolve from microarray gene expression to copy‑number variation, DNA‑binding protein profiling, and next‑generation sequencing data, while providing tools for searching, browsing, downloading, and visualizing studies at gene or study level. Today GEO stores over 20,000 functional genomics studies and remains the primary source for direct high‑throughput data submissions. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Abstract

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/ .