Best approach for Gene Ontology characterization

[sr320]

What are folks preferred means to annotate gene sets with gene ontology information as well as how do you perform Gene Enrichment Analyses?
any links to code would be appreciated.

[cascoamarillo]

Hi Steven (@sr320) ,
I was hoping someone else with more recent analysis experience will chime in (there were a few talks/posters with GO terms in EpiMar22!). I did this back in 2019, so probably there are better ways; more streamline and easier for non-models.
In the case of Rotifers, for every gene set generated (species, isolate, etc) I had to run all steps to get the GO annotations (ie. two isolates from the same species can have slightly different gene sets from annotation).

I have used the Trinotate package (https://github.com/Trinotate/Trinotate/wiki). I run it in a computing cluster. Otherwise the blastx/blastp steps (just followed https://github.com/Trinotate/Trinotate/wiki/Software-installation-and-data-required) could have take too long. Once you have the Gene-GO association, it can be used for further analysis on different scenarios (RNA-seq, genes methylated, etc) with their in-house script run_GO_Seq. Though Trinotate is a continuation workflow for Trinity (denovo transcriptome assembly), it can be used (as I did) for gene annotations from genome assemblies (eg. Braker).

I hope this helps.
Best,
Fernando

[snbogan]

A relevant plug for anyone following this thread - we just began drafting a tutorial and method comparison related to gene/functional enrichment analyses. Here are the draft markdown and its knit.