Post Analysis Tutorial


This quick tutorial will guide you through the creation of an additional gene-set on a pre-existing Enrichment Map. It can for example help to localize microRNA, transcription factors or drug targets in enriched pathways displayed on the map. The new gene-set that we want to add to the network is called the signature gene-set.

Download the test data:

Description of the tutorial files contained in the PostAnalysisTutorial folder:

  • CTCF_DIFF.gmt Signature gene-set.
  • Human_GO_AllPathways_no_GO_iea_April_15_2013_symbol.gmt Gene-set file used to create the original Enrichment Map
  • ES12_EM_example.cys The Enrichment Map on which we want to add the signature gene-set


  1. Open Cytoscape and Open ES12_EM_example.cys
  2. Click on Plugins / Enrichment Map/ Post Analysis
  3. Please select the following files by clicking on the respective (…) button and selecting the file in the Dialog:
    • GMT / ‘Human_GO_AllPathways_no_GO _iea_April_15_2013_symbol.gmt’
    • SigGMT / ‘CTCF_DIFF.gmt’
  4. Click on Load Gene-Sets
    • In the Signature-Genesets box: click on CTCF_DIFF as available Signature-Genesets
    • Click on the down arrow to move CTCF_DIFF in the lower box
  5. Tune parameters
    • Set Number of common genes to 20
  6. Click on Run

Examining Results


  • The yellow triangle is the signature gene-set and the pink edges represent overlap of 20 genes or more between the signature gene-set and a given gene-set from the Enrichment Map (red node). The width of the pink edges is proportional to the number of genes in the overlap.
  • This signature gene-set represents the CTCF (transcription factor) target genes that are different in MCF7 cells treated or not with Estrogen.
  • Clicking on a pink edge will show the genes contained in this overlap in the gene expression panel:


The gene-signature gene-set corresponds to ENCODE CHIP-seq data for the cell line MCF-7 treated or not with estrogen and for the CTCF factor using the tool CSCAN/Browse data ( The signature gene-set includes the genes that were different between the two conditions (treated or not with estrogen)