I want to ask about gene ontology analysis.
So, I have around 1,200 transcription factor genes ID (EnsEMBL id). I have done some clustering on a different constraint and I want to see the result of my cluster in the GO context. The only problem here is because all of them transcription factor, I always get transcription factor related ontology as the top. Because all of them are TF, of course ontology analysis will produce the result. What I want is to find ontology other than that so I know what kind of function this cluster works together, for example related to cancer development, stem cell, etc.
My question is, what kind of tools or script that I can use or make to filter out the transcription factor related ontology? Now, I am using DAVID and several other online tools. If possible, I want to develop my own script in python so that I can easily repeat that GO analysis for all my cluster that I found.