KEGG database for GSEA
I am working on Chicken RNA-Seq dataset. I want to do enrichment analysis using GO and KEGG databases. I read and tried the protocol given in this paper, which recommends GSEA and gprofiler.
GSEA uses human gene sets. I thought of downloading GMT files from gprofiler website to prepare custom dataset to use in GSEA. But gprofiler does not allow downloading of KEGG files due to licensing issues.
How can use my gene list to find enriched KEGG pathway and import Please suggest a protocol or tutorial to find enriched KEGG pathways and use the output as input for cytoscape for visualization.
Thank you!
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This may be useful if you are comfortable with an R-based approach: MSigDB for Multiple Organisms in a Tidy Data Format