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 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
2. Click on Plugins / Enrichment Maps / Load Enrichment Results
3. Make sure the Analysis Type is set to GSEA
4. 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 " 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

5. P-value cut-off 0.001

6. Q-value cut-off 0.05

7. Check Overlap Coefficient

8. Overlap coefficient cut-off 0.5

9. Build Enrichment Map
10. Go to View, and activate Show Graphics Details
11. Go to the Viz Mapper, and switch the labels mapping to EM1_GS_DESCR

Version 0.4 or earlier

Mac

1. Open Cytoscape
2. Click on Plugins / Enrichment Maps / Load GSEA Results

3. Please select the Gene Set file (.gmt)... GO_Hs_EG_f_hgu133p2.gmt

4. Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... MCF7_ExprMx.txt

5. Please select the Generic result file for first dataset... EnrTable_12h_E2.xls

6. Please select the Generic result file for first dataset... EnrTable_12h_NT.xls

7. OPTIONAL:Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... NONE

8. (OPTIONAL) Please select the Generic result file for first dataset... EnrTable_24h_E2.xls

9. (OPTIONAL) Please select the Generic result file for first dataset... EnrTable_24h_NT.xls

10. P-value cut-off 0.001

11. FDR Q-value cut-off 0.05

12. Check Overlap Coefficient

13. Overlap coefficient cut-off 0.5

14. Build Enrichment Map
15. Go to View, and activate Show Graphics Details
16. 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
2. Click on Plugins / Enrichment Maps / Load GSEA Results

3. Please select the Gene Set file (.gmt)... GO_Hs_EG_f_hgu133p2.gmt

4. Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... MCF7_ExprMx.txt

5. Please select the Generic result file for first dataset... EnrTable_12h_E2.xls, EnrTable_12h_NT.xls

6. OPTIONAL:Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... NONE

7. (OPTIONAL) Please select the Generic result file for first dataset... EnrTable_24h_E2.xls, EnrTable_24h_NT.xls

8. P-value cut-off 0.001

9. FDR Q-value cut-off 0.05

10. Check Overlap Coefficient

11. Overlap coefficient cut-off 0.5

12. Build Enrichment Map
13. Go to View, and activate Show Graphics Details
14. Go to the Viz Mapper, and switch the labels mapping to EM1_GS_DESCR

Expected Result

Network stats:

• 188 nodes
• 745 edges

Network Topology:

• 

• warning: global rotational discrepancies are expected due to stochasticity in the layout algorithm

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