Gene Expression Omnibus (GEO)

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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: Differential systems – e.g. cancer vs. normal, drug vs. no drug Choose/prepare the microarray Extract total mRNA (transcriptome) Reverse transcription/dye labeling Combine equal amounts Hybridize Scan 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 GPL GSM GSE GDS Submitted by Experimentalists Manufacturer Curated by NCBI GPL Platform descriptions GSM Raw/processed spot intensities from a single slide/chip GSE Grouping of slide/chip data “a single experiment” GDS Grouping of experiments

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