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. 2007 Jan;35(Database issue):D760-5.
doi: 10.1093/nar/gkl887. Epub 2006 Nov 11.

NCBI GEO: mining tens of millions of expression profiles--database and tools update

Tanya Barrett  1 , Dennis B Troup, Stephen E Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F Kim, Alexandra Soboleva, Maxim Tomashevsky, Ron Edgar
Affiliations

NCBI GEO: mining tens of millions of expression profiles--database and tools update

Tanya Barrett et al. Nucleic Acids Res. 2007 Jan.

Abstract

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/

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Figures

Figure 1
Figure 1
A selection of GEO screenshots from a typical experiment (GEO DataSet GDS877; 16). (A) DataSet record includes experiment summary information, DataSet subset classifications, and access to data mining features such as hierarchical cluster heat map and ‘Query subset A versus B’ tool. (B) DataSet hierarchical cluster heat map calculated by un-centered correlation coefficient/average linkage option. Regions of interest can be selected using the red image cropper box, then either expanded to view sample and gene annotation, downloaded, charted as line plots, or linked directly to corresponding Entrez GEO profiles records. (C) GEO profiles retrieval results; each entity includes sequence identifier and DataSet information, and a thumbnail profile image. (D) Expanded profile chart depicts expression value information for the crystallin gene across each sample in DataSet GDS877. Experimental subset groupings are reflected in labels at foot of chart.
Figure 2
Figure 2
A schematic overview of query workflow, and how various features and tools are interlinked. A description of the location and purpose of these features is provided in Table 1.
See this image and copyright information in PMC

References

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