Question: GO Term enrichment with poor number of GO Terms
0
gravatar for Macspider
2.1 years ago by
Macspider2.8k
Vienna - BOKU
Macspider2.8k wrote:

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.

ADD COMMENTlink modified 2.1 years ago by Jean-Karim Heriche18k • written 2.1 years ago by Macspider2.8k

What should someone do in these situations?

My advice would be to generate more data!

ADD REPLYlink written 2.1 years ago by Benn6.8k

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.

ADD REPLYlink written 2.1 years ago by Macspider2.8k

actually for everything that is not human, mouse, fly, thaliana

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.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Jean-Karim Heriche18k

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.

ADD REPLYlink written 2.1 years ago by Macspider2.8k

do you have any suggestions on other tests that I should/could do?

What question are you trying to address ? Do you have any hypothesis ? How did you arrive at this gene list ?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Jean-Karim Heriche18k

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).

ADD REPLYlink written 2.1 years ago by Macspider2.8k
1
gravatar for Jean-Karim Heriche
2.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

If by "poorly annotated", you mean that the genes are not well annotated with GO terms, you can increase GO terms coverage by transferring annotation by orthology, i.e. any gene in your species of interest that has annotated orthologs inherits the GO terms from these orthologs.

ADD COMMENTlink written 2.1 years ago by Jean-Karim Heriche18k

The numbers I provided are already after that stage :(

ADD REPLYlink written 2.1 years ago by Macspider2.8k
1

You can push this by looking at more distantly related species and/or by relaxing orthology to homology.

ADD REPLYlink written 2.1 years ago by Jean-Karim Heriche18k
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