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    Gene Expression Omnibus

    Category  Genomics>Gene Expression Databases/Tools

    Abstract  The Gene Expression Omnibus (GEO) is a gene
    expression/molecular abundance public repository that archives and
    freely distributes high throughput gene expression data submitted by
    the scientific community. GEO currently stores approximately a billion
    individual gene expression measurements, derived from over 100
    organisms, addressing a wide range of biological issues. These huge
    volumes of data may be effectively explored, queried, and visualized
    using Web-based tools.

    GEO Architecture
    Submitters supply their gene expression data in four (4) sections - 1)
    Platform - describes the list of features on the array (e.g., cDNAs,
    oligonucleotides, etc.);  2) Sample - describes the biological material
    and the experimental conditions under which the sample was handled,
    and the abundance measurement of each feature derived from it; 3)
    Series - defines a set of related Samples that are considered to be part
    of an experiment; 4) Supplementary data - original microarray scan
    images or raw quantification data.
    Sample data are assembled into biologically meaningful and
    comparable GEO DataSets. DataSet records provide a coherent
    synopsis about an experiment and form the basis of GEOs data display
    and analysis tools.

    GEO Submissions
    An infrastructure is provided in which submitters can supply MIAME
    (Minimum Information About a Microarray Experiment)-compliant data.
    There are four (4) ways in which data may be deposited with GEO - 1)
    Web deposit - simple, step-by-step, interactive Web forms; 2)
    Spreadsheets - Excel spreadsheet templates for batch deposit; 3)
    SOFT (Simple Omnibus Format in Text) - a plain text, line-based format
    designed for rapid batch submission; 4) MINiML (MIAME Notation in
    Markup Language) - an XML format designed for rapid batch
    submission.

    Data Mining
    The data in GEO can be queried using two (2) NCBI Entrez databases -
    1) Entrez GEO-DataSets - provides an experiment-centric view of the
    data in GEO. Experiments of interest may be located by searching for
    attributes such as free text keywords, technology type, author,
    organism, and experimental variable information. Once a relevant
    DataSet is identified, that experiment can be further explored for gene
    expression profiles of interest using the supplementary tools provided
    on the GEO DataSet record.

    Tools available on the GEO DataSet record - a) Cluster heat maps - A
    selection of hierarchical and K-means clustering algorithms are
    provided. Clusters of interest can be selected, enlarged, downloaded,
    plotted as line charts, or linked directly to Entrez GEO-Profiles; b) Query
    subset A vs. B - This tool assists in the identification of genes that
    display marked differences in expression level between two specified
    sets of Samples within a DataSet, as calculated using t-tests or fold
    difference. Genes that meet the user-defined criteria are presented in
    Entrez GEO-Profiles; c) Subset effects - This feature retrieves all
    profiles that are flagged as having significant effects with respect to a
    specific experimental variable, for example 'age' or 'strain'.

    2) Entrez GEO-Profiles - provides a gene-centric view of the data in
    GEO. Gene expression profiles of interest may be located by searching
    for attributes such as gene name, GenBank accession number, SAGE
    tag, GEO accession number, description, or profiles flagged as having
    significant effects with regards to specific experimental variables.

    Tools available within Entrez GEO-Profiles results page - a) Profile
    neighbors - returns a list of genes that show a similar expression
    pattern within a given DataSet; b) Sequence neighbors - retrieves
    profiles related by nucleotide sequence similarity by BLAST;
    c) Homolog neighbors - retrieves profiles of genes belonging to the
    same HomoloGene group; d) Links - Links to other NCBI Entrez
    databases including GenBank, PubMed, Gene, UniGene, OMIM,
    Homologene, Taxonomy, SAGEMap, and MapViewer.

    Note: The data in GEO can also be queried outside of the Entrez
    databases with GEO BLAST - The GEO BLAST interface allows you to
    search for GEO-Profiles of interest based on nucleotide sequence
    similarity. Additionally, all standard BLAST results display 'E' icons that
    link directly to GEO-Profiles expression data. And more.


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    National Library of Medicine
    Building 38A
    Bethesda, MD 20894
    USA
    Voice: (301) 496-2475
    Fax:    (301) 480-9241
    info@ncbi.nlm.nih.gov
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