Question

gene set enrichment in clusterprofiler

1

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2.8 years ago

Omics data mining ▴ 260

Hello everyone

I would like to do functional gene set enrichment analysis in clusterProfiler via gseGO and gseKEGG. These function needs a list of genes, which I'm planning to rank by log fold change. Should the gene list contain all genes, or should it just contain genes below a significance cut off (e.g. padj < 0.05)?

I would appreciate all the suggestions

clusterprofiler gene enrichment analysis set • 2.1k views

ADD COMMENT • link updated 2.8 years ago by MRezaei ▴ 40 • written 2.8 years ago by Omics data mining ▴ 260

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Its common to set only the significant genes (padj < 0.05) and separate them between upregulated and downpregulated genes (logFC >1.0 or logFC <-1.0)

ADD REPLY • link 2.8 years ago by Vitor1 ▴ 120

score 2 · Answer 1 · 2022-02-20

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2.8 years ago

gglim ▴ 210

You should use all the expressed genes as the input of GSEA. That's difference between normal DA (differential analysis) and GSEA.

ADD COMMENT • link 2.8 years ago by gglim ▴ 210

score 0 · Answer 2 · 2022-02-14

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2.8 years ago

cvenkat95 ▴ 10

I would suggest you try both, and compare the results. Processing for pathway analysis does not take much time anyway.

ADD COMMENT • link 2.8 years ago by cvenkat95 ▴ 10

score 0 · Answer 3 · 2022-02-21

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2.8 years ago

MRezaei ▴ 40

My previous answer was due to a misunderstanding, so I deleted it to avoid possible mistakes. It would be best to use all of the genes in the dataset as the input of GSEA analysis. The GSEA analysis contains DE analysis by itself.

ADD COMMENT • link 2.8 years ago by MRezaei ▴ 40