How ti identify genes per terms in with topGO for scRNAseq dataset

Question

[camillab.]

Hi all,

I want to to perform Gene Ontology (GO) Enrichment of Genes Expressed in specific clusters and I am following this tutorial but in the output I cannot find which genes are associated per terms. How do I find them?

Also (more theoretical question) is it correct to perform GO in a subset of cluster (eg. all cluster expressing a specific marker regardless the cell type)?

Thank you very much!

Camilla

[AHerik]

To find the genes associated with the gene ontology term, I would look up the exact GO term in this dataset (https://www.gsea-msigdb.org/gsea/index.jsp). That's usually how I do it. If you want a pathway analysis pathway with good visualizations, look into SCPA (https://jackbibby1.github.io/SCPA/).

For your second question, I'm not sure what you're asking. Are you asking about the validity of performing pathway analysis in one of your clusters, with a comparison between two conditions? Or do you want to perform pathway analysis on ANY cell expressing your gene of interest?

[camillab.]

thank you very much! (I have missed the reply for some reason)

I am asking what it is the best practice for pathway analysis in scRNAseq when you have an integrated dataset? Do I have to do it for each cluster? for the whole dataset or can I do it for all cells expressing X genes (eg. Sox2+ cells which corresponds to maybe a couple of clusters)?