Get gene embedding for gene similarity using TransformerGO

[hoangthienan95]

Hi there,

Thank you for the really interesting paper and model. I'm working through the paper and repo, so I apologize if the answer to my question is really obvious and I have missed it. I have a custom gene-to-GO annotations. How can I use TransformerGO to get an embedding of genes based on their GO annotation to do analysis on gene similarity based on GO annotations? Which resource should I look at first?

Thank you!

[Ieremie]

I'm so sorry, I'm seeing this just now.

What you want to do is to first embed the GO terms using the node2vec framework. If you are using a new version of the Gene Ontology graph you might want to train node2vec again.

You can then use one of the trained models to do the predictions or train a new one on the new embeddings.