Is there a tool to obtain GO terms for thousands of genes at once?

Question

[Ana]

I have run a permutation analysis on genetic interactions and I am trying to see if the biology of the significant ones is more relevant than the non-significant interaction's biology. To do that and since there is no literature for most of the interactions, I have searched for each interacting gene's GO terms and then found the ones that overlap. My issue is that I need to run a random distribution analysis to check whether the frequency of overlap is more significant than in randomly generated pairs. To do this, I need to obtain the biological info (i.e., GO terms) of around 1000 random pairs to run my permutations. Does anyone know of a tool that allows for that? Thanks in advance!

[Ana]

Is there a tool to do this but with KEGG pathways instead? Thanks.

[GenoMax]

GeneSCF may be an option: https://github.com/genescf/GeneSCF?tab=readme-ov-file#Step-by-step-instructions

Please be aware that use of KEGG database requires a license for extensive use.

Answer 1

[GenoMax]

a tool to obtain GO terms for thousands of genes at once?

Check out genescape by @Istvan : https://github.com/ialbert/genescape-central

Specifically: https://github.com/ialbert/genescape-central?tab=readme-ov-file#genetrack-annotation

[Ana]

Thank you so much

[Istvan Albert]

YESS! That's what it is for. You can plug in thousands of genes, visualize them, and filter away. I use this tool so much in my work.

[Ana]

Do you know whether there is a way to filter the GO terms based on the number of mapped genes they have? I am interested only in GO terms that have less than 400-500 genes. Thanks in advance.

[Istvan Albert]

The tool draws all ancestors for a term. I would say that, in general, it would be hard to avoid drawing common terms. Because they will still be in the tree, typically, these terms are low-level generic words like "binding" that remain in the subtree if there is at least one more term at a deeper level.

Post an image of what you have and what you'd like removed, and I'll better understand your goals.

[Ana]

I got it figured out, thanks!