Hi all,
I have a set of around 250 genes which I'm testing and among everything I am trying I also decided to check if they're enriched for particular GO Terms or gene families. Sadly, I am not working with a well annotated organism, so my GO Term mapping on my genes actually returned only 20% of the genes as covered by GO Terms.
What should someone do in these situations? Are there any tools that try to extend the GO Term coverage with some particular (idk, just guessing) homology modelling?
Also, do you have any suggestions on other tests that I should/could do? I have the functional annotation for each of these sequences, so I am now manually checking the annotated function but I would like to know if there are cool tools to do that automatically.
My advice would be to generate more data!
My problem is not with my data, but with the paucity of GO Terms for non-canonical organisms (actually for everything that is not human, mouse, fly, thaliana). I was wondering if I was missing something.
This sounds like you didn't use annotations from model organisms. If so why ? Model organisms have the most and best annotations so you should make use of it.
It is the next step. But first, I wanted to ask what I asked here to be sure that I didn't have any other chance.
What question are you trying to address ? Do you have any hypothesis ? How did you arrive at this gene list ?
This set of genes host potentially disruptive variants and I already have the proof that the expression is not disrupted. The function however may be. I'm trying to see if they're enriched for any particular function, process or component (i.e. GO terms).