gene expression omnibus (geo)
Post on 28-Dec-2015
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A public repository for the archiving and distribution of gene expression data submitted by the scientific community.
MIAME compliant data. Minimum Information About a Microarray Experiment
http://www.mged.org/Workgroups/MIAME/miame.html
Convenient for deposition of gene expression data, as required by funding agencies and journals.
Curated, online resource for gene expression data browsing, query, analysis and retrieval.
Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data Repository
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
Submitters may provide raw data
Original microarray scans Raw quantification data
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
GEO Home Page
Simple interface to: show status
find documentation query data browse data submit data
Basic Search: Repository Browser
Selecting the total public data or Repository Browser links on the GEO home page, takes you to the Repository Browser, listing: number of each type of submitted file, both public and unreleased the total number of each technology type under Platforms the total number of each Sample type
Basic Search: Browse Platforms
All GEO submissions need to be associated with a platform file. These describe the features on a given platform, required to understand the data.
A platform file must be submitted if one is not already present in GEO. Commercial array platform files are submitted to GEO by the manufacturer.
Basic Search: Browse Platforms
Accession:GEO ID
Title:brief description
of platform
Contact:submitter
Samples:number of samples in GEO associated
with platform ID
Technology:platform
type
Release date:when file is
publicly accessible
The table can be sorted on any field except organism by clicking on the header.Specific platform files can be found using the ‘Find Platform’ option.
Basic Search: Find Platforms
Select ‘Find Platform’ Select company Select distribution Select species Enter title keyword
Basic Search: Find Platforms (continued)
Start the platform search Select the accession for the U133 plus 2.0 array Scroll down to find data table information
Data Retrieval: Browse Series
Data is submitted to GEO as a Series, which represents the experiment design.
Selecting Browse>Series brings up a list sorted by release date. Selecting a Series ID brings up the Series file summary.
GEO Accession Results Display Options
Scope controls what information is displayed:SelfPlatform, Samples or SeriesFamily
Format controls how information is displayed:HTMLSOFT (Simple Omnibus Format in Text)MINiML (MIAME Notation in Markup Language)
Amount controls how much information is displayed:Brief QuickFull Data
All GEO accession results pages have the same header that allows different views and formats for the data to be displayed
Data Retrieval: Series Accession Page
Biological sample summary
Design summary
Publication information
Platform (total)
Samples (total)
Data Retrieval: Sample File Summary
Sample preparation
Hybridization and data
processing
Platform Series
Data Retrieval: Sample File Data TableData table field
descriptions
Truncated data table from Quick view
Total data rows and file size
Supplementary raw data file
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.
Advanced Searches
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
Total results
Number of DataSets
Number of Platforms
Number of Series
DataSet Search Result
DataSet ID
Description
Platform
Reference Series
Supplementary files
Number of Samples and truncated list
Cluster image
Select the DataSet ID or click on the cluster image to go to the DataSet record.
GEO DataSet Record
Experiment design and DataSet information.
Sample and analysis information. Data retrieval.
Selecting analysis takes you to the data clustering interface.
Selecting the cluster image takes you to the clustering page
GEO Gene Profiles
GEO DataSet ID
Platform ID, Platform Feature ID
Gene description
Target sequence accession
Expression profile
GEO Gene Profiles use gene IDs from Platform files to show the expression of a gene across DataSets.
Entering a gene ID into the Query>Gene profiles text box takes you to the Entrez results page.
GEO BLAST
On the GEO BLAST page enter sequences in fasta format, GenBank accessions or select sequence files on local disks for blastn comparisons.
These are compared to GenBank sequences listed in Platform files associated with GEO DataSets
From the Blast result page select the ‘E’ option to the right of an alignment to show GEO Gene Profiles for that sequence in GEO DataSets
E button
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