GO enrichment in non-model organism

Question

[neethav]

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!

[Michael]

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 mailing 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.

Answer 1

[mikhail.shugay]

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

• Trinotate
• Blast2GO
• TRAPID