How test for significant overlap in GO Ontology annotations, between two gene sets; used ShinyGo KEGG and Biol Proc
I have two lists of genes, the genome-wide significant hits from 2 diseases. I did gene ontology in ShinyGo, for KEGG pathways, and Biological Processes, to see if there was significant overlap in the sets of annotations between the two diseases. I am unsure as to the best statistical test to use for an unexpectedly (significantly) high level of overlap in the two sets of annotations. Thanks!
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Can you confirm the exact data that you are aiming to compare? - like, literally, paste an example here, please?. Is it p-values and / or text data (the 'text data' being the KEGG pathway and Biological Processes).