Have you thought about performing GOSlim analyses? Here you can find what GOSlim stands for "GO slims are cut-down versions of the GO ontologies containing a subset of the terms in the whole GO. They give a broad overview of the ontology content without the detail of the specific fine grained terms."

There are some GOSlims sets already defined (see link above) but you can always define your own set of GO terms to perform the GOSlim analysis.

In this kind of analysis you start with a set of GO terms and a set of selected terms that we'll call GOSlim set (for example). You then see (browsing the GO Graph) if each of the GO Terms is connected with any term of the GOSlim set. In other words, you translate all the GO terms you have initially into a set of selected (normally of interest) GO terms.

HTH. Marina