qPCR results and enrichment analysis with comparison

Question

[pavan.mathur]

I need a few suggestions from Cytoscape experts. I have qPCR results (60 genes) with fold change and log value too, and I want to perform enrichment analysis (gprofiler and Cytoscape or any software you can suggest). I have never done that kind of analysis before. I was watching people comments and videos but still, can’t figure out how to put my data for enrichment analysis in Cytoscape and how to camper group vice. I have this kind of data; please advise me how I can proceed better way to analysis.

        g-A   g-B        g-C            g-D        g-E

Foxo3   1   1.10558405  0.84134146  0.98463419  0.79779405
Foxo4   1   2.2111681   1.93289511  1.24056134  3.58197417
IL1b    1   5.4445345   0.34967745  0.74621318  0.64801013

[ATpoint]

Enrichment against what? Which question you want to answer?

Answer 1

[scooter]

As the previous comment suggested, you need to first figure out what your question is. For example, say your g-B column represents a condition fold change and your g-E column represents some treatment condition fold change. And you're interested in seeing what terms best describe the genes where g-B is up-regulated and g-E is down-regulated. In Cytoscape, you would do that by using an app like the stringApp to create a network, then create a filter that would select the nodes of interest and then use STRING's enrichment. On the other hand, if you are looking to find enriched terms for a set of genes that have similar expression patterns across all columns g-B:g-E, then I think you'll want to use something like GSEA (https://www.gsea-msigdb.org/gsea/index.jsp), which doesn't use Cytoscape at all.