Gene Expression Omnibus (GEO)

The Gene Expression Omnibus (GEO) is a publicly-funded repository of gene-expression studies maintained by the NCBI. Access the repository here.

There is lots of help documentation for the GEO repository. This page provides an overview of how GEO records are structured, and explains the differences between GEO Platforms, Samples, Series and DataSets.

Here we focus on analyzing GEO data in GEO Datasets and in in using GEO Series for Differential Gene Expression (DEG) analysis

Using the GEO web interface to identify differentially expressed genes in gene-expression datasets

See the video tutorial here

• Select a data set
  • e.g. GSE44097
  • Click 'Analyze with GEO2R'
  • Define groups of samples (e.g. treated and control)
  • Assign samples to groups
  • Click 'Top 250' to give you list of differentially expressed genes