Gene Set Enrichment Analysis (GSEA) plugin

This is a short description of a plugin for GSEA in maps hosted in MINERVA. The plugin calculates enrichment for uploaded data overlays. Public overlays are available for GSEA to all the users. User-provided (private) overlays can be analyzed only when a given user is logged in.


Load the plugin

Use the plugin icon to invoke the plugin popup, and paste the address of the plugin in the URL field (see figure below). The address of the plugin is: https://minerva-dev.lcsb.uni.lu/plugins/gsea/plugin.js
Press UPLOAD button to start the plugin.

Load


Plugin functionality

To use the plugin, select from the left panel the overlay for which you would like to calculate the enrichment. Then, press the Show enriched pathways button.

Use

The figure above shows the results of the plugin:

  1. The overlay, for which GSEA is calculated is “Braak 1-2”. A reminder: you need to be log in to see your own overlays.
  2. The results of the enrichment: the p-value is Bonferroni adjusted. The Enriched area column contains the names of pathways and submaps, for which are enriched in the considered overlay. Enriched areas are highlighted in the map.


Remarks

  • The names of the pathways are not visible for the highlighted areas. Switch back to Pathways and compartments view to see the names.
  • If multiple overlays are selected, the enrichment will be calculated for the union of the corresponding gene sets.
  • The single elements behind the highlighted area are not clickable. Press Reset button to remove the highlighting.