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.
- Clicking on a pink edge will show the genes contained in this overlap in the gene expression panel:
Note: 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 (http://159.149.160.51/cscan/). The signature gene-set includes the genes that were different between the two conditions (treated or not with estrogen)