I'm having a bit of confusion about how can I retrieve all the genes that are associated to a specific gene ontology.
Lets say I need to find all the genes that are associated with this GO entry:
GO:0030098 lymphocyte differentiation
This is the graph representing the parents of my GO. In the same page I find the Child Terms that represent the children of my term.
Now, I can download the goa file (related to the organism I'm interested into) containing the GO associations and
grep my term to extract a list of associated genes but, as far as I can understand, this list does not represent the whole graph that actually describe my GO term.
Should I also get the genes in the childred terms of my term? Or in the parents terms? If yes, then again I have to go back in the graph and find the parents/children of the found parents/children and so on, till the whole graph is visited.
Is this the correct approach? Or should I only focus on those genes related to my GO:0030098, and that's it?
I found this: Retrieving a list of human genes having GO associations and this but I think they don't address my question since they do not describe the parent-children association.
Also I found this, on the GO FAQ, but what I need to do is quite the opposite.
Summarising: I need to find the genes associated to a specific GO term. Should I also look for its parents or children or not?