Download - Gene Expression Omnibus (GEO)
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Gene Expression Omnibus (GEO)
http://www.ncbi.nlm.nih.gov/geo/
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Microarrays in gene expression
A typical gene expression analysis experiment:1. Differential systems – e.g. cancer vs. normal, drug vs. no
drug2. Choose/prepare the microarray3. Extract total mRNA (transcriptome)4. Reverse transcription/dye labeling 5. Combine equal amounts6. Hybridize7. Scan8. ANALYSE AND INTERPRET THE RESULTS – this is
the tricky part…
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Microarrays in gene expression
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SPOTS
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Hybridization
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SCAN
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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.
Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data Repository
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GEO Architecture
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 has four kinds of data records
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GPLPlatform
descriptions
GSMRaw/processedspot intensities
from a singleslide/chip
GSEGrouping of
slide/chip data“a single experiment”
GDSGrouping ofexperiments
Curated byNCBI
Submitted byExperimentalistsSubmitted by
Manufacturer
GEO Architecture
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GEO Home Page
Simple interface to: show status
find documentation query data browse data
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Platform Accession Page
•Platform details:
•Description
•Type
•Organism
•Manufacturer
•Related samples and
series
NOTE THE TOP BAR (SCOPE)
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Sample Accession Page
•Sample details:
•Description
•Type
•Organism
•Source
•Related
platforms and
series
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Sample File Data TableData table field
descriptions
Truncated data table from Quick view
Total data rows and file size
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Series Accession Page
•Biological sample summary
•Design summary
•Publication information
•Related platforms and samples
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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
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Querying GEO DataSets
Start a GEO DataSets search with the Query>DataSets text box This brings up an Entrez GEO DataSets results form
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DataSet Search Results
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GEO DataSet Record
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GENE PROFILE search
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GEO Gene Profiles
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GEO Gene Profiles
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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
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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.
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GEO BLAST