I have a Chipseq data with peak coordinates that I want to overlay with 3 public data sets associated with the same protein. I have used bed tools to intersect coordinates to check the overlap of my data with public datasets. I was wondering if it is reasonable do the Go/ pathway analysis with peaks of public datasets and overlapping peaks of my dataset and look for common biological terms. Since the definition of gene may be different so I can assign common distance in both datasets (public and mine) and will provide more meaningful biological insight. On the other side since peaks are overlapping (not exactly but with few bases) it can be argued that both peaks (public and my dataset) will have the same pathways. I can use
GREAT for this purpose. Any suggestion will that be a reasonable approach to look for consensus Go terms or not? BTW I am not asking for my assignment. I thought about it and googled it but did not find any paper showing what I am thinking. So I am requesting expert feedback from the community.