Gene Expression Omnibus GEO http www ncbi nlm
Gene Expression Omnibus (GEO) http: //www. ncbi. nlm. nih. gov/geo/
Microarrays in gene expression n A typical gene expression analysis experiment: 1. 2. 3. 4. 5. 6. 7. 8. Differential systems – e. g. cancer vs. normal, drug vs. no drug Choose/prepare the microarray Extract total m. RNA (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 n A public repository for the archiving and distribution of gene expression data submitted by the scientific community. n Curated, online resource for gene expression data browsing, query, analysis and retrieval. n Convenient for deposition of gene expression data, as required by funding agencies and journals.
GEO Architecture GEO has four kinds of data records n Platform (GPL) = the technology used and the features detected. n Sample (GSM) = preparation and description of the sample. n Series (GSE) defines a set of samples and how they are related. n Data. Sets (GDS) sample data collections assembled by GEO staff.
GEO Architecture Submitted by Manufacturer GPL Platform descriptions Submitted by Experimentalists GSM GSE Grouping of Raw/processed slide/chip data spot intensities from a single “a single experiment” slide/chip Curated by NCBI 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: n Datasets: experiment-centric view using Entrez GEO Data. Sets n Gene profiles: gene-centric view using Entrez GEO Profiles Selecting either takes you to a similar Entrez introduction page
Querying GEO Data. Sets n n Start a GEO Data. Sets search with the Query>Data. Sets text box This brings up an Entrez GEO Data. Sets results form
Data. Set Search Results
GEO Data. Set Record
GENE PROFILE search
GEO Gene Profiles
GEO Gene Profiles
Querying GEO with IDs from Papers n n n 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 Pub. Med Search Results n n One option for displaying Pub. Med search results is GEO Data. Set links. When present, the results page is actually from Entrez GEO Data. Sets.
GEO BLAST
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