[19] Gene Expression Omnibus: Microarray Data Storage, Submission, Retrieval, and Analysis

Abstract

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of both unprocessed and processed data in a MIAME-(Minimum Information About a Microarray Experiment) supportive infrastructure that promotes fully annotated submissions. GEO currently stores about a billion individual gene expression measurements, derived from over 100 organisms, submitted by over 1,500 laboratories, addressing a wide range of biological phenomena. To maximize the utility of these data, several user-friendly Web-based interfaces and applications have been implemented that enable effective exploration, query, and visualization of these data, at the level of individual genes or entire studies. This chapter describes how the data are stored, submission procedures, and mechanisms for data retrieval and query. GEO is publicly accessible at http://www.ncbi.nlm.nih.gov/projects/geo/.

Upregulation of NEK2 is associated with drug resistance in ovarian cancer

“…The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data, predominantly gene expression data generated by DNA microarray technology (23). By 2006, GEO stored approximately a billion individual gene expression measurements, derived from over 100 organisms, submitted by over 1,500 laboratories, addressing a wide range of biological phenomena (81). Thus, the expression data of NEK2 in ovarian cancer tissues and drug-resistant cells retrieved from the two online databases are reliable.…”

Next Generation Sequencing - Advances, Applications and Challenges

“…In addition to the published sequence and array based datasets stored in public repositories such as GEO [54], a number of datasets are pre-loaded in public Genome Browsers. For example, the UCSC Genome Browser provides access to data from the ENCODE project [55], including expression data in the form of RNA-seq and regulatory data generated through ChIP-seq representing several different cell lines and various primary tissue types.…”

Genome Profiling and Potential Biomarkers in Neurodegenerative Disorders

“…Raw data from all microarray experiments listed in Table 1 was obtained directly from Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) utilizing the GEOquery package for R [20,21]. Before the meta-analysis of data from selected studies was performed, all the datasets obtained in such manner were inspected for significant inter-array differences in distribution of probe intensities.…”