Pathways Analysis in R

Question

[GiuliaAC]

Hi!

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!

[Jan Oosting]

You could use the globaltest bioconductor package

[Morris_Chair]

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

[GiuliaAC]

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.

[Jan Oosting]

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

[Hamid Ghaedi]

Check this new thread: C: for go enrichment analysis which tool do you recommend?

Answer 1

[xanderpico]

There are a lot of options. Here are a couple specific recommendations:

• clusterProfiler - actively maintained R package with great documentation. Includes built-in support for GO analysis, but can also plugin GMT files from WikiPathways or even of your own creation.

• rSEA - one of the newer options in this space. According to their paper, it resolves a lot of statistical issues with prior approaches. It's also flexible enough to use with GO, WikiPathways or your own GMTs. Note: this method, uses p-values from all genes in your DE analysis (not just a pre-selected subset of DEGs).