Functional enrichment in differentially expressed genes from RNA-seq

Question

[Les Ander]

Hi guys

I have googled and also searched biostar but I haven't found a complete answer yet.

I am new to R and can really appreciate your help.

I want to know in my set of differentially expressed genes, what is the enrichment for Gene ontology function or pathway. I have come across other posts that mention good/popular packages in R (Best UPDATED tool for enrichment anlysis) but I don't know enough of R to be able to stitch together the output I have from DSeq and then into the gene set enrichment package to get the list of enriched function. I use the DAVID go ontology online but would really like to learn to use it from within R.

So, this is what I have so far.

I imported the counts_table (which was measured using bedtools multicov), and used DSeq to identify differentially expressed genes. The relevant part is

res=nbinomTest(cds,"treated","untreated")
FDR_THRESHOLD=0.05
resSig=res[res$padj< FDR_THRESHOLD,]
namesSig=na.omit(res[res$padj<FDR_THRESHOLD,])$id

So now I have an array of enriched human genes, with names in genesymbol format, in the namesSig array.

My question: Can you please show me an example of how I can go about finding the enrichment of genes using any reliable gene set enrichment package in R?

Thank you

Answer 1

[Sukhi Singh]

Hi Les,

This will get you started Statistical analysis and visualization of functional profiles for genes and gene clusters.

Basic steps,

1. Install and load clusterProfiler package.
2. Convert the gene symbols to entrez id's using bitr and then run the enrichGO function.

Cheers

[Les Ander]

Thank you so much