GSEA heatmap for all genes?
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5.3 years ago
biopat • 0

Hi all,

I was wondering if it is possible to have the GSEA program to show all genes in one heat map. I know the whole point is for it to find the enrichment in certain pathways, but I would like to have a heat map that shows the differential expression of all genes. I have 4 different samples. A wildtype, GeneA KO, GeneB KO, and GeneAB KO.

If there is another way to do this I would appreciate it, if you you share that as well!

Thank you!

GSEA RNA RNA-Seq heat map • 2.5k views
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If you need to do it in GSEA specifically, you can create a custom pathway that includes all genes and run GSEA with it. It will be really long, though.

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Like "all" genes? So about 25000* genes?

*give or take a few thousands depending on your definition and source of annotation

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