Question: Enrichment analysis of Differentially expressed genes
gravatar for Ambika
12 months ago by
United States/Auburn/Auburn University
Ambika20 wrote:

Hello everyone,

I used STAR-HTseq-DESeq2 pipleline to analyse my RNAseq data and now I have list of differentially expressed genes. I want to do the enrichment analysis of the list of genes obtained from DEseq2. I tried to use DAVID but it didn't work for me since I am working with non-model organism (fungi). Could you please suggest any other programs that are good for enrichment analysis with non model organisms.

Thank you, Ambika

ADD COMMENTlink written 12 months ago by Ambika20

Is there a published genome for your organism? Is it annotated?

edit: just as a side note, HTSeq is not needed here, because STAR can output counts with the parameter --quantMode GeneCounts.

ADD REPLYlink modified 12 months ago • written 12 months ago by h.mon24k

No it is not published and not annotated

ADD REPLYlink written 12 months ago by Ambika20
gravatar for h.mon
12 months ago by
h.mon24k wrote:

Are you still working with the same fungi as here: Extract exon Intron reads from RNA seq data ? You have an assembled draft genome, a gtf with predicted genes, and mapped your RNAseq to this draft genome? Assuming so, you will have to annotate this genome somehow. A quick and dirty annotation would just be blasting / diamonding the Augustus predicted genes against UniProt, to associate each gene with a UniProt identifier. Then you could use DAVID.

Another quick and dirty option would be to map your RNAseq to a close, annotated genome - in case one exists. Tthis way you can leverage the existing annotation to perform enrichment analysis.

ADD COMMENTlink written 12 months ago by h.mon24k

Yes you are right I have an assembled draft genome. Right now I am trying to blast my draft genome using Blast2Go and looks like it will take forever. I will try the other idea you said using UniProt. Thank you h.mon for helping.

ADD REPLYlink written 12 months ago by Ambika20

Hi, h.mon, I was looking on how can I associate each identified gene with UniProt identifier, but I am lost. Can you suggest a way I can do that.

ADD REPLYlink written 12 months ago by Ambika20
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