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Learning Outcomes
  • Understand the concept of Gene Set Enrichment Analysis (GSEA).
  • Learn to launch GSEA Explorer in both stand-alone and report tab modes.
  • Identify input requirements and advanced options in GSEA Explorer.
  • Explore the output results of GSEA analysis.

GSEA Explorer Tutorial

Gene Set Enrichment Analysis (GSEA) is designed to evaluate whether a specific gene set or pathway is enriched in gene expression data, highlighting its potential biological relevance to the condition under study. The method is based on the premise that relevant gene sets or pathways will show coordinated changes in expression rather than changes in individual genes.

Launching GSEA Explorer

You can launch the GSEA Explorer application in two ways: stand-alone mode or through Foundry's RNA-sequencing pipeline or the Differential Expression module.

Launching in Stand-alone Mode

  1. In the top banner, click on Apps, then select the Shared Apps tab.
  2. Search for GSEA Explorer or locate the app in the displayed table.
  3. Click the Launch button.

Launching from the Report Tab

  1. Navigate to the Report tab.
  2. Select any .Rmd file; the specific file does not affect the launch.
  3. Click the Launch button in the GSEA Explorer card.

Inputs

In the inputs section on the right side, select the corresponding species. The DESeq results from your run and the GMT file will be available in their respective dropdowns. If additional inputs are required, you can upload them to either the Inputs or GMT directory in the GSEA Explorer section of the Reports tab by clicking the + sign above the launch script.

Advanced Options

Gene Set Size

You can define the minimum and maximum number of genes allowed in a gene set. Gene sets that fall outside these bounds will not be processed.

Fold Change Shrinkage

You have the option to toggle the use of log₂FoldChange and shrunken log₂FoldChange if fold change shrinkage was applied after running DESeq. It is generally recommended to use shrunken log₂FoldChanges in GSEA.

Outputs

In the main panel, the GSEA results will display the following information for each gene set:

  1. Gene set name
  2. Number of genes in the gene set
  3. Normalized Enrichment Score
  4. Adjusted p-value

Selecting a specific row will display the corresponding enrichment plot on the right side and highlight the leading edge genes at the bottom of the panel.