stringApp enrichment analysis: Brief introduction to the GSEA functionality of Cytoscape stringApp
Channel: Lars Juhl Jensen
Date: 2021-09-20

A brief introduction to the gene set enrichment analysis (GSEA) functionality of Cytoscape stringApp, an app that brings the functionality of the STRING data to Cytoscape. The presentation gives an overview of the categories of gene sets included and how to use a custom background, filter results, and visualize them on a network. If you are not familiar with enrichment analysis, I recommend watching my short introduction to the core concepts of enrichment analysis (https://youtu.be/2NC1QOXmc5o) before watching this presentation.

0:00 Introduction: Cytoscape stringApp and gene set enrichment analysis
0:28 Functional enrichment: categories of gene sets and the STRING enrichment table
1:05 Enriched publications: text mining, publications as gene sets, and the STRING publications table
1:30 Choosing the background: genome-wide background and user-provided custom backgrounds
2:13 Cluster annotation: network clustering and enrichment analysis of selection against full network
2:45 Filtering and visualization: filtering by category, removal of redundant terms, enrichment visualization on networks, and export of enrichment results to EnrichmentMap or files.

Hands-on exercises on Cytoscape and stringApp are available at https://jensenlab.org/training/stringapp/