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GEO (Gene Expression Omnibus) Deepak Sambhara Georgia Institute of Technology 21 June, 2006 What is GEO? Why Use GEO? Background and Significance QUERY Search QUERY Results Browsing Demo Features A gene expression repository created by the NCBI Located: /projects/geo Supports data submissions, browsing, query and retrieval. Organized on three levels: platforms, series, and samples Validating PADRE by invalidating public data Thorough data for microarray experiments Designing interface of MAGMA MIAME (Minimum Information About a Microarray Experiment) Compliant Effort to help standardize publicly available data /Workgroups/MIAME/ MIAME CHECKLIST Experimental Design Samples used, extract preparation and labeling Hybridization procedures and parameters Measurement data and specifications Array Design 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 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 Can browse by data sets (Result page with all experiments) or GEO Accessions GEO Accessions browsed by Platforms, Samples, or Series /projects/geo GO TO Search data sets for “cancer” Download .CEL files Click GEO Accession link to access experiment Take note of chip platform Find the corresponding .pdf document using PubMed IDs Take note of Classes, and number of arrays Download DataSet file (Raw data) and Annotation file DataSet SOFT file list gene expression for all patients Web-based analysis through Heirarchial Clustering, Value Distributions and t-tests Can plot selected gene profiles using a region of interest box Click v