Enrichment Map Post Analysis Tutorial

Outline

This quick tutorial will guide you through the creation of an additional gene-set on an 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.

To run this tutorial:

• You need to have Cytoscape installed : minimally 2.6.3 must be installed but preferable to have the latest version of Cytoscape 2 (e.g. 2.8.3)
• It does not work with Cytoscape 3
• Install the Enrichment Map plugin from the Cytoscape plugin manager. If you install it manually (e.g. if you need to install a new version that doesn't happen to be in the plugin manager yet), then it must be in the Cytoscape-[Version#]/plugins folder

• You need to download the test data: PostAnalysisTutorial.zip

Description of the tutorial files contained in the PostAnalysisTutorial folder:

• CTCF_DIFF.gmt : List of the genes included in the signature gene-set.

• Human_GO_AllPathways_no_GO_iea_April_15_2013_symbol.gmt: Original gene-set file that has been used to create the original Enrichment Map

• ES12_EM_example.cys: the Enrichment Map on which we want to add the signature gene-set

Instructions

• 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

ES12_EM_example_PA_CTCF_Diff.cys

• 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.