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

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…

Microarrays in gene expression

SPOTS

Hybridization

SCAN

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

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

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

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 TableData 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