#acl All:read

{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>> 
= Enrichment Map Post Analysis Tutorial =
<<TableOfContents(3)>>

= 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: [[attachment: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 =
{{attachment:PostAnalysis_screenshot.png|Screenshot PostAnalysis EM Panel|align="right"}} 

  *1. '''Open Cytoscape''' and '''Open ES12_EM_example.cys'''

<<BR>>
  *2. Click on '''Plugins''' / '''Enrichment Map'''/ '''Post Analysis'''
<<BR>>
  *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'

<<BR>>
  *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

<<BR>>
  *5. '''Tune parameters'''
      * Set '''Number of common genes''' to 20
  *6.  Click on '''Run'''


<<BR>><<BR>>
== Examining Results ==
[[attachment:ES12_EM_example_PA_CTCF_Diff.cys]]

<<BR>>
{{attachment:PostAnalysisMap_screenshot.png}} 
 * 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:
{{attachment:PostAnalysisMap_DataPanel.png}} 

 * 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)