grouping gene ontology parent-child terms

Question

[clementine]

Hello everyone,

Sorry if this is posted before, I've searched through the posts but none of them made me reach the solution, maybe I've missed it.

I have performed pathway over-representation on a set of genes and now trying to visualize the enrichment. However, I also want to filter out too specific gene ontology terms and also pick the parent term (when a parent and some child terms are present).

I have tried to do some visualizations with ClueGO and BiNGO by setting the maximum and minimum levels I wanted but could not get the clear results I wanted. That's why I'd like to group them first by keeping the parent one among my results. Does anyone know a tool that would make it for me? Otherwise, I feel like I need to check the GO ancestry of all of them one-by-one and decide to keep/remove manually which I assume would take quite a bit of time :)

Answer 1

[Jean-Karim Heriche]

Late answer that might still be useful. A recurrent issue with ontologies is that terms relevant to the question at hand are often at different levels of the ontology and many branches of the ontology may be irrelevant. One way to deal with this is to use a slim ontology, i.e. a subset of the ontology tailored to the question/domain of interest. You can either use already available GO slim ontologies or create your own. Another way is simply to select a list of relevant terms and use it as a flat controlled vocabulary.