GSEA results obtained using a 'pre-ranked' file (NO GMT file) - how do I run Enrichment Map in Cytoscape - in the absence of a GMT file?
Enrichment Map requires a ranked genes and a gene set in GMT format.
GMT file is nothing but a text file with genes belonging to a pathway or a particular functional category. It's very easy to create a GMT file from a gene list. They provide some gene sets here
Hey, I have pre-ranked data as well which is obtained by GSEA. You can use the .GMT file in the .edb file present.
In addition, you can use the protocol written in the following paper: Nat Protoc. 2019 Feb;14(2):482-517. doi: 10.1038/s41596-018-0103-9. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. Reimand J1,2, Isserlin R3, Voisin V3, Kucera M3, Tannus-Lopes C3, Rostamianfar A3, Wadi L1, Meyer M1, Wong J3, Xu C3, Merico D4,5, Bader GD6,7,8.
You need the following Softwares: 1. Java Standard Edition (http://www.oracle.com/technetwork/java/javase/ downloads/index.html) is required to run GSEA and Cytoscape. 2. GSEA desktop application (http://software.broadinstitute.org/gsea/ downloads.jsp) is used for pathway enrichment analysis . 3. The Cytoscape desktop application (http://www.cytoscape.org/download.php), as well as the following Cytoscape applications, is required for enrichment map visualization: EnrichmentMap, v.3.1 or higher; clusterMaker2, v.0.9.5 or higher; WordCloud, v.3.1.0 or higher; AutoAnnotate, v,1.2.0 or higher. These can be conveniently downloaded and installed together by installing the ‘EnrichmentMap Pipeline Collection’ (http://apps.cytoscape.org/apps/ enrichmentmappipelinecollection) from the Cytoscape App Store.
Then in your GSEA, go to ENRICHMENT FILE VISUALISATION Then open Cytospace as well in the GSEA: there is the column of locate your GSEA files: put the edb file and just click on build enrichment file.
You shall get the map. :)
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