This is a test version of Biostars. For the public version, visit https://www.biostars.org.
gene set enrichment in clusterprofiler

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
• 3,186 views • link
updated by MRezaei • MRezaei • written by Omics data mining Omics data mining

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)

• 0 views • link
written by vitor • vitor

3 answers

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

• 0 views • link
written by gglim • gglim

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

• 0 views • link
written by cvenkat95 • cvenkat95

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.

• 0 views • link
written by MRezaei • MRezaei

Log in to answer this question.

More posts like this