September 23, 2015

To Download Program:

Launch gsea.jnlp

Set Preferences

..

Workflow for Gene Set Enrichment Analysis

  • 3 Control and 3 Condition - use preranked rather than Gene Expression Matrix
  • Use t-statistic derived from more powerful ANOVA analysis
  • Make sure to take the maximum absolute t-statistic for each gene (in case of duplicate gene symbols)
  • Output should contain only unique gene symbols with t-statistic (*.rnk format)

Load Data (Ranked Gene List)

Ranked Gene List by t-statistic (GSEA gene list.rnk)

   replace "///.*\t" with "\t"

Load File

Run GSEA Preranked method

Select Database from GSEA Website

Set up Parameters for Run

Option to change cpu usage

Look at GSEA Report

Snapshot - Upregulated Genes

Snapshot - Downregulated Genes

Look at Downregulated Results

Click on Geneset –> Website

Click on Details of Cell Cycle Process

Additional Analyses

  • Go back to parameters window and select additional gene sets and re-run

The End