Question: GO enrichment in non-model organism
4
gravatar for neethav
5.6 years ago by
neethav40
United States
neethav40 wrote:

Hi all,

 I am working on a RNA-seq study of a non-model organism. I have used local BLASTx to identify orthologous genes from different closely related organisms, and now have a list of GO terms associated with my transcripts. I now want to do a GO enrichment analysis of differentially expressed transcripts from my study. Is there any program that does GO enrichment with input files containing just GO terms and the ID of the gene? I know that GOEAST does this, but wanted to know if there is any other option out there.

Thanks!

go rna-seq enrichment • 4.9k views
ADD COMMENTlink modified 5.5 years ago by Michael Dondrup47k • written 5.6 years ago by neethav40

Bumping for interest. I also have the impression that most tutorials and manuals treat this use-case very poorly if at all. For example for Bioconductor packages most seem to rely on a list of geneids to either download the annotation or use an existing BioC annotation package. It even seems very hard to determine if a package can deal with self defined term annotations at all. Possibly we should have a list of BioC packages that can.

I found this https://stat.ethz.ch/pipermail/bioconductor/2011-February/037834.html as a thread on the BioC mailling list, but it doesn't look straight-forward to extract the required steps. I suggest that the documentation of most such packages could use some improvement.  

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Michael Dondrup47k
1
gravatar for mikhail.shugay
5.6 years ago by
mikhail.shugay3.4k
Czech Republic, Brno, CEITEC
mikhail.shugay3.4k wrote:

The following tools may be worth a try, although they will require some re-analysis

ADD COMMENTlink modified 9 weeks ago by RamRS25k • written 5.6 years ago by mikhail.shugay3.4k
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