Bioinformatics Shared Resource Introduction to Gene Expression Omnibus (GEO) bsrweb.sanfordburnham.org

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Presentation transcript:

Bioinformatics Shared Resource Introduction to Gene Expression Omnibus (GEO) bsrweb.sanfordburnham.org

GEO Database: Public repository that archives and distributes expression data Microarray data and Next-gen Sequencing Data; RNA-seq User-friendly Web based tools to explore data Approximately a billion measurements recorded and available to search 100 organisms and thousands of different expression analysis platforms GEO expression data submission Pre-requisite for publications including expression data Step by step web deposit Proper preparation of sample data spreadsheets and submission forms GEO query Use search terms (text) to locate relevant DataSets or gene profiles Search for and download complete sets of data (including raw array data) Provides on-the-fly data analysis using the built in R stats tools (interesting!) bsrweb.sanfordburnham.org

GEO database structure The data is carefully structured around - platforms - the array type - samples - the single sample on a chip -series - the grouping of samples These are the basic building blocks of GEO

Linked data tables make a GEO record Affymetrix chip GPL570 HG-U133plus2 Time point at X hrs The samples grouped to make a Series or DataSet

How to find data in GEO Study level Gene Level GDS4165 Exp profiles of homologs Curated DataSets The Complete Lists

After locating data: download ALL data and files, inc platform WARNING! These formats can be inconsistent ALL data and files in XML values of the expression data reliable approach: download the RAW files (chp files for Affy, idat for illumina) and reprocess them

Key words in Search box

Study type in Search box

Select by Study Type and Organism Link to short read archive Compressed txt files

GEO DataSet Analysis Tools Compare 2 sets of samples (T-tests) Precomputed Cluster Heatmaps R analysis for differentially expressed genes LIVE DEMO!!!!

GEO2R: Analyze GEO microarray Data retrieve a list of differentially expressed genes Use search to find datasets of interest

Click on Link to GEO2R

The R tool in GEO

With help from Bioinformatics Shared Resource Format and submit datasets to GEO Large scale statistical analysis Wide variety of analytical techniques (TFBS search) Advanced data plotting for figures Sequence Analysis (RNA-seq)