## page was renamed from Software/EnrichmentMap/Tutorial
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#acl All:read
{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>> 
= Enrichment Map Tutorial =

== Outline ==

This quick tutorial will guide you through the generation of an Enrichment Map for the microarray data-set: Estrogen Treatment of MCF7 Breast Cancer Cells (12 and 24 hours).

Pre-requisites:
    * Cytoscape >= 2.6.3 must be installed
    * The Enrichment Map plug-in must be in the Cytoscape-v2.6.x/plugins folder
    * Download the test data 

Go this page [[Software/EnrichmentMap|to download the plugin and the test data]] 

== Data Description ==

    * Gene Ontology gene-set collection (`GO_Hs_EG_f_hgu133p2.gmt`)
    * expression matrix (`MCF7_ExprMx.txt`)
    * enrichment tables
          * dataset-1
                * treated, 12hrs (`EnrTable_12h_E2.xls`)
                * untreated, 12hrs (`EnrTable_12h_NT.xls`) 
          * data-set 2
                * treated, 24hrs (`EnrTable_24h_E2.xls`)
                * untreated, 24hrs (`EnrTable_24h_NT.xls`) 

== Instructions ==
=== Version 0.5 or newer ===

   1. Open Cytoscape
   1. Click on Plugins / Enrichment Maps / Load Enrichment Results
   1. Make sure the Analysis Type is set to GSEA
   1. Please select the following files by clicking on the respective (...) button and selecting the file in the Dialog:
      * Gene Sets / GMT: `GO_Hs_EG_f_hgu133p2.gmt`
      * Dataset 1 / Expression: `MCF7_ExprMx.txt`
      * Dataset 1 / Enrichments 1: `EnrTable_12h_E2.xls`
      * Dataset 1 / Enrichments 2: `EnrTable_12h_NT.xls`
      * Click on "''Dataset 2 {{attachment:arrow_collapsed.gif}}''" to expand the panel
      * Dataset 2 / Expression: ''leave empty''
      * Dataset 2 / Enrichments 1: `EnrTable_24h_E2.xls`
      * Dataset 2 / Enrichments 2: `EnrTable_24h_NT.xls`
   1. P-value cut-off `0.001`
   1. Q-value cut-off `0.05`
   1. Check Overlap Coefficient
   1. Overlap coefficient cut-off `0.5`
   1. Build Enrichment Map
   1. Go to View, and activate Show Graphics Details 
   1. Go to the Viz Mapper, and switch the labels mapping to EM1_GS_DESCR

=== Version 0.4 or earlier ===
==== Mac ====

   1. Open Cytoscape
   1. Click on Plugins / Enrichment Maps / Load GSEA Results
   1. Please select the Gene Set file (.gmt)... `GO_Hs_EG_f_hgu133p2.gmt`
   1. Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... `MCF7_ExprMx.txt`
   1. Please select the Generic result file for first dataset... `EnrTable_12h_E2.xls`
   1. Please select the Generic result file for first dataset... `EnrTable_12h_NT.xls`
   1. OPTIONAL:Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... `NONE`
   1. (OPTIONAL) Please select the Generic result file for first dataset... `EnrTable_24h_E2.xls`
   1. (OPTIONAL) Please select the Generic result file for first dataset... `EnrTable_24h_NT.xls`
   1. P-value cut-off `0.001`
   1. FDR Q-value cut-off `0.05`
   1. Check Overlap Coefficient
   1. Overlap coefficient cut-off `0.5`
   1. Build Enrichment Map
   1. Go to View, and activate Show Graphics Details 
   1. Go to the Viz Mapper, and switch the labels mapping to EM1_GS_DESCR

Ontology term names (whereas the default option displays the GO IDs)

==== PC ====

   1. Open Cytoscape
   1. Click on Plugins / Enrichment Maps / Load GSEA Results
   1. Please select the Gene Set file (.gmt)... `GO_Hs_EG_f_hgu133p2.gmt`
   1. Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... `MCF7_ExprMx.txt`
   1. Please select the Generic result file for first dataset... `EnrTable_12h_E2.xls`, `EnrTable_12h_NT.xls`
   1. OPTIONAL:Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... `NONE`
   1. (OPTIONAL) Please select the Generic result file for first dataset... `EnrTable_24h_E2.xls`, `EnrTable_24h_NT.xls`
   1. P-value cut-off `0.001`
   1. FDR Q-value cut-off `0.05`
   1. Check Overlap Coefficient
   1. Overlap coefficient cut-off `0.5`
   1. Build Enrichment Map
   1. Go to View, and activate Show Graphics Details 
   1. Go to the Viz Mapper, and switch the labels mapping to EM1_GS_DESCR

== Expected Result ==

__Network stats:__

    * 188 nodes
    * 745 edges 

__Network Topology:__

    {{attachment:EBC_Sample_GO.png}}
    * warning: global rotational discrepancies are expected due to stochasticity in the layout algorithm