GEO by liwenting

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									Gene Expression Omnibus (GEO)




    http://www.ncbi.nlm.nih.gov/geo/
    Microarrays in gene expression

   A typical gene expression analysis experiment:
    1.   Differential systems – e.g. cancer vs. normal, drug vs. no
         drug
    2.   Choose/prepare the microarray
    3.   Extract total mRNA (transcriptome)
    4.   Reverse transcription/dye labeling
    5.   Combine equal amounts
    6.   Hybridize
    7.   Scan
    8.   ANALYSE AND INTERPRET THE RESULTS – this is
         the tricky part…
Microarrays in gene expression
SPOTS
Hybridization
SCAN
Gene Expression Omnibus (GEO):
Gene Expression and Molecular Abundance Data Repository

   A public repository for the archiving and
    distribution of gene expression data submitted by
    the scientific community.

   Curated, online resource for gene expression
    data browsing, query, analysis and retrieval.

   Convenient for deposition of gene expression
    data, as required by funding agencies and
    journals.
GEO Architecture
            GEO has four kinds of data records

   Platform (GPL) = the technology used and the features
    detected.

   Sample (GSM) = preparation and description of the
    sample.

   Series (GSE) defines a set of samples and how they
    are related.

   DataSets (GDS) sample data collections assembled by
    GEO staff.
   GEO Architecture

                       Submitted by
Submitted by          Experimentalists                Curated by
Manufacturer                                            NCBI

  GPL             GSM                GSE                GDS
  Platform     Raw/processed       Grouping of        Grouping of
descriptions   spot intensities   slide/chip data     experiments
                from a single “a single experiment”
                  slide/chip
    GEO Home Page




Simple interface to:

 show status

 find documentation

 query data

 browse data
   Platform Accession Page


•Platform details:

    •Description

    •Type

    •Organism

    •Manufacturer

    •Related samples and

    series

NOTE THE TOP BAR (SCOPE)
   Sample Accession Page


•Sample details:

    •Description

    •Type

    •Organism

    •Source

    •Related

    platforms and

    series
 Sample File Data Table
     Data table field
       descriptions



Truncated data table
    from Quick view




Total data rows and
             file size
  Series Accession Page



•Biological sample summary


•Design summary

•Publication information


•Related platforms and
samples
DATASET or GENE PROFILE search




GEO data can be queried as:
   Datasets: experiment-centric view using Entrez GEO DataSets

   Gene profiles: gene-centric view using Entrez GEO Profiles



Selecting either takes you to a similar Entrez introduction page
    Querying GEO DataSets




   Start a GEO DataSets search with the Query>DataSets text box
   This brings up an Entrez GEO DataSets results form
DataSet Search Results
GEO DataSet Record
GENE PROFILE search
GEO Gene Profiles
GEO Gene Profiles
    Querying GEO with IDs from Papers




   A common way to access GEO data is through accessions from papers.
   Online journals include hyperlinks to the GEO accession page.
   Or, at the GEO home page enter the accession into the Query>GEO
    accession text box
    GEO Links in PubMed Search Results




   One option for displaying PubMed search results is GEO DataSet links.
   When present, the results page is actually from Entrez GEO DataSets.
GEO BLAST

								
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