Question: Functional enrichment in differentially expressed genes from RNA-seq
0
gravatar for Les Ander
2.3 years ago by
Les Ander100
United States
Les Ander100 wrote:

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 stich 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

 

 

 

ADD COMMENTlink modified 2.3 years ago by Sukhdeep Singh9.0k • written 2.3 years ago by Les Ander100
3
gravatar for Sukhdeep Singh
2.3 years ago by
Sukhdeep Singh9.0k
Netherlands
Sukhdeep Singh9.0k wrote:

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

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Sukhdeep Singh9.0k

Thank you so much

ADD REPLYlink written 2.3 years ago by Les Ander100
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