Question: Pathways Analysis in R
gravatar for GiuliaAC
5 weeks ago by
GiuliaAC0 wrote:


I would like to perform a pathway analysis in R. In particular, I have the genes signatures (that define pathways) that I want to investigate. I have just perform the differential expression analysis between the conditions. I would like to know, using ONLY deg, which signatures are enriched.

Thank you for your help!

R deg pathways • 124 views
ADD COMMENTlink modified 5 weeks ago by volidif6590 • written 5 weeks ago by GiuliaAC0

You could use the globaltest bioconductor package

ADD REPLYlink written 5 weeks ago by Jan Oosting920

Hi Julia, you may want to use genecodis or DAVID tool for this type of analysis by selecting the more expressed and significant genes

ADD REPLYlink written 5 weeks ago by Morris_Chair190

But in this way I can only investigate public signatures (such as gene ontology terms, reactome etc.), right?

But I have some signatures, that I defined, that I want to investigate in a differential expression analysis that I performed.

ADD REPLYlink written 5 weeks ago by GiuliaAC0

You can use your own signatures with these types of tests, because they're basically repeated chi-square, or Fisher exact tests, where you test whether the proportion of DEG is different between the population and your signature. i.e You test 20000 genes of which 200 ( 1%) are DE, your signatures contains 100 genes of which 10 are DE (10%) the Fisher exact test will tell you if this difference in proportion is significant. i

ADD REPLYlink written 5 weeks ago by Jan Oosting920
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