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)
- dataset-1
Instructions
Version 0.5 or newer
- Open Cytoscape
- Click on Plugins / Enrichment Maps / Load Enrichment Results
- Make sure the Analysis Type is set to GSEA
- 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
P-value cut-off 0.001
Q-value cut-off 0.05
- Check Overlap Coefficient
Overlap coefficient cut-off 0.5
- Build Enrichment Map
- Go to View, and activate Show Graphics Details
- Go to the Viz Mapper, and switch the labels mapping to EM1_GS_DESCR
Version 0.4 or earlier
Mac
- Open Cytoscape
- Click on Plugins / Enrichment Maps / Load GSEA Results
Please select the Gene Set file (.gmt)... GO_Hs_EG_f_hgu133p2.gmt
Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... MCF7_ExprMx.txt
Please select the Generic result file for first dataset... EnrTable_12h_E2.xls
Please select the Generic result file for first dataset... EnrTable_12h_NT.xls
OPTIONAL:Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... NONE
(OPTIONAL) Please select the Generic result file for first dataset... EnrTable_24h_E2.xls
(OPTIONAL) Please select the Generic result file for first dataset... EnrTable_24h_NT.xls
P-value cut-off 0.001
FDR Q-value cut-off 0.05
- Check Overlap Coefficient
Overlap coefficient cut-off 0.5
- Build Enrichment Map
- Go to View, and activate Show Graphics Details
- 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
- Open Cytoscape
- Click on Plugins / Enrichment Maps / Load GSEA Results
Please select the Gene Set file (.gmt)... GO_Hs_EG_f_hgu133p2.gmt
Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... MCF7_ExprMx.txt
Please select the Generic result file for first dataset... EnrTable_12h_E2.xls, EnrTable_12h_NT.xls
OPTIONAL:Please select the dataset (.gct) or (.rpt) file used for GSEA analysis... NONE
(OPTIONAL) Please select the Generic result file for first dataset... EnrTable_24h_E2.xls, EnrTable_24h_NT.xls
P-value cut-off 0.001
FDR Q-value cut-off 0.05
- Check Overlap Coefficient
Overlap coefficient cut-off 0.5
- Build Enrichment Map
- Go to View, and activate Show Graphics Details
- Go to the Viz Mapper, and switch the labels mapping to EM1_GS_DESCR
Expected Result
Network stats:
- 188 nodes
- 745 edges
Network Topology: