GEO (Gene Expression Omnibus)
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Transcript of GEO (Gene Expression Omnibus)
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GEO (Gene Expression Omnibus)
Deepak Sambhara
Georgia Institute of Technology
21 June, 2006
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What is GEO?
-A gene expression repository created by the NCBI
-Located: http://www.ncbi.nlm.nih.gov/projects/geo
- Supports data submissions, browsing, query and retrieval.
- Organized on three levels: platforms, series, and samples
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Why Use GEO?
- Validating PADRE by invalidating public data
- Thorough data for microarray experiments
- Designing interface of MAGMA
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Background and Significance
-MIAME (Minimum Information About a Microarray Experiment) Compliant
-Effort to help standardize publicly available data
-http://www.mged.org/Workgroups/MIAME/
MIAME CHECKLIST
-Experimental Design
-Samples used, extract preparation and labeling
-Hybridization procedures and parameters
-Measurement data and specifications
- Array Design
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QUERY Search- Search by Data Sets, Gene profiles, GEO Accession numbers, or GEO Blast
-Can modify queries using search tabs on results page
- Search tabs: limits, history, clipboard, and query translation
E.g. Filter for only experiments with .CEL files
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QUERY Results- Listed by relevance; sortable by: datasets, platforms and series
-Up to 500 results per page; shows summary of experiment, can list by briefs, PubMed links etc.
- If .CEL files exist, downloadable on results page.
- Click GEO accession number to access experiment page
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Browsing
- Can browse by data sets (Result page with all experiments) or GEO Accessions
-GEO Accessions browsed by Platforms, Samples, or Series
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Demo
http://www.ncbi.nlm.nih.gov/projects/geo
GO TO
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Search data setsfor “cancer”
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Download .CELfiles
Click GEO Accessionlink to access experiment
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Take note of chip platform
Find the corresponding .pdf document using PubMed IDs
Take note of Classes, and number of arrays
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Download DataSet file (Raw data) and Annotation file
DataSet SOFT filelist gene expressionfor all patients
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Web-based analysis through Heirarchial Clustering, Value Distributions and t-tests
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Can plot selected gene profiles using a region of interest box
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Click value distribution for distribution of avg. gene expression values for outlier detection
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One or two-tailed t-tests completed to compare two classes in the experiment
SignificanceLevels can beadjusted from 0.001 to 0.100
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Shows Probe Set ID’s found significant based on chosen class comparisons
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Features
PROS CONS- User-friendly interface
- MIAME Compliant
- Web based analysis
- Raw data/Annotation files available
- Vastly expansive/thorough compared to other microarray databases
- GSE series/ GDS series differences
- Must have PubMed ID
- .CEL files not available for all datasets
- .CEL files are individually zipped
- No Quality Control Information