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!
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written
by
GiuliaAC •
1 answer
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).
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Hi Julia, you may want to use genecodis or DAVID tool for this type of analysis by selecting the more expressed and significant genes
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.
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
You could use the globaltest bioconductor package
Check this new thread: C: for go enrichment analysis which tool do you recommend?