Producing Enrichment map using KEGG pathways

[Amin Ali]

Hi there,

I am new to Cytoscape and I been reading/watching videos of the enrichment map. I was wondering if there is a step by step guide in producing something like this:

Currently I have the gene list with FDR and logFC as well as the GSEA KEGG and Reactome results. 

Please advise

[Ruth Isserlin]

HI Amin, 

The best step by step guide is the nature protocol that goes through the whole Enrichment map pipeline: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6607905/

There is also an updated version of the nature protocol that you can find here: https://baderlab.github.io/EnrichmentMap_Protocol/

Thanks, 

Ruth 

On Wed, Mar 3, 2021 at 6:13 PM Amin Ali <angk...@gmail.com> wrote:

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