GO Term enrichment with poor number of GO Terms
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4.3 years ago
Macspider ★ 3.4k

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.

Gene Ontology GO Terms Annotation InterPro • 1.2k views
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What should someone do in these situations?

My advice would be to generate more data!

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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.

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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.

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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.

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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 ?

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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).

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4.3 years ago

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.

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The numbers I provided are already after that stage :(

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

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