Database Commons a catalog of biological databases

Database Commons - GEO

GEO

Citations: 9384

z-index 205.27

Short name GEO
Full name Gene Expression Omnibus
Description The Gene Expression Omnibus is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community.
URL http://www.ncbi.nlm.nih.gov/geo/
Year founded 2002
Last update & version 2015-12-30    
Availability Free to all users
University/Institution hosted National Center for Biotechnology Information
Address Bethesda,MD 20892,USA
City Bethesda
Province/State MD
Country/Region United States
Contact name Tanya Barrett
Contact email barrett@ncbi.nlm.nih.gov
Data type(s)
Major organism(s)
Keyword(s)
  • functional genomics
  • NGS
Publication(s)
  • NCBI GEO: archive for functional genomics data sets--update. [PMID: 23193258]

    Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko, Andrey Yefanov, Hyeseung Lee, Naigong Zhang, Cynthia L Robertson, Nadezhda Serova, Sean Davis, Alexandra Soboleva
    Nucleic acids research 2013:41(Database issue)
    860 Citations (Google Scholar as of 2016-05-09)

    Abstract: The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.

  • Strategies to explore functional genomics data sets in NCBI's GEO database. [PMID: 22130872]

    Stephen E Wilhite, Tanya Barrett
    Methods in molecular biology (Clifton, N.J.) 2012:802
    10 Citations (Google Scholar as of 2016-05-09)

    Abstract: The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies. Data sets are submitted to GEO primarily by researchers who are publishing their results in journals that require original data to be made freely available for review and analysis. In addition to serving as a public archive for these data, GEO has a suite of tools that allow users to identify, analyze, and visualize data relevant to their specific interests. These tools include sample comparison applications, gene expression profile charts, data set clusters, genome browser tracks, and a powerful search engine that enables users to construct complex queries.

  • NCBI GEO: archive for functional genomics data sets--10 years on. [PMID: 21097893]

    Tanya Barrett, Dennis B Troup, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Rolf N Muertter, Michelle Holko, Oluwabukunmi Ayanbule, Andrey Yefanov, Alexandra Soboleva
    Nucleic acids research 2011:39(Database issue)
    769 Citations (Google Scholar as of 2016-05-09)

    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/.

  • NCBI GEO: archive for high-throughput functional genomic data. [PMID: 18940857]

    Tanya Barrett, Dennis B Troup, Stephen E Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F Kim, Alexandra Soboleva, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Rolf N Muertter, Ron Edgar
    Nucleic acids research 2009:37(Database issue)
    805 Citations (Google Scholar as of 2016-05-09)

    Abstract: The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that 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' (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

  • NCBI GEO: mining tens of millions of expression profiles--database and tools update. [PMID: 17099226]

    Tanya Barrett, Dennis B Troup, Stephen E Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F Kim, Alexandra Soboleva, Maxim Tomashevsky, Ron Edgar
    Nucleic acids research 2007:35(Database issue)
    1045 Citations (Google Scholar as of 2016-05-09)

    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/

  • NCBI GEO standards and services for microarray data. [PMID: 17160034]

    Ron Edgar, Tanya Barrett
    Nature biotechnology 2006:24(12)
    88 Citations (Google Scholar as of 2016-05-09)

    Abstract:

  • Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. [PMID: 16939800]

    Tanya Barrett, Ron Edgar
    Methods in enzymology 2006:411
    330 Citations (Google Scholar as of 2016-05-09)

    Abstract: The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information 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 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 1500 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 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/.

  • Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. [PMID: 16888359]

    Tanya Barrett, Ron Edgar
    Methods in molecular biology (Clifton, N.J.) 2006:338
    75 Citations (Google Scholar as of 2016-05-09)

    Abstract: 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. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret the hundreds of microarray studies and millions of gene expression patterns stored in GEO. Data can be examined from both experiment-centric and gene-centric perspectives using user-friendly tools that do not require specialized expertise in microarray analysis or time-consuming download of massive data sets. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

  • NCBI GEO: mining millions of expression profiles--database and tools. [PMID: 15608262]

    Tanya Barrett, Tugba O Suzek, Dennis B Troup, Stephen E Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex E Lash, Wataru Fujibuchi, Ron Edgar
    Nucleic acids research 2005:33(Database issue)
    839 Citations (Google Scholar as of 2016-05-09)

    Abstract: The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30,000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

  • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. [PMID: 11752295]

    Ron Edgar, Michael Domrachev, Alex E Lash
    Nucleic acids research 2002:30(1)
    4563 Citations (Google Scholar as of 2016-05-09)

    Abstract: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

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Tags

Expression
Archaea Bacteria Eukaryota Virus
functional genomics NGS

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-04-11]
    • Lin Liu [2016-03-29]
    • Lin Liu [2016-03-25]
    • Lina Ma [2015-12-30]
    • Jian Sang [2015-12-05]
    • Jian Sang [2015-06-28]
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