I have a list of prokaryotic genes and I will annotate them with GO terms. Nevertheless, because of the characteristics of my dataset, I do not have gene IDs. So, I would like to perform GSEA, because some of these genes fall in some categories and some genes fall in other categories. So, I could have, for example, a dataset like this:
Category 1 Category 2 Category 3
Gene1 GO:X 50 24 2
Gene2 GO:X 89 7 8
Gene3 GO:X 67 14 12
Gene4 GO:X 25 10 19
Nevertheless, I think that I should interpret results category by category, so I could also have the same data but one file per Category:
Category 1
Gene1 GO:X 50
Gene2 GO:X 89
Gene3 GO:X 67
Gene4 GO:X 25
These datasets would be only a small proportion of a larger dataset, so this is only a selection because these genes are significantly associated to one or another category.
However, I can only find tools that ask for universal gene IDs for GSEA analyses (such as ncbi IDs, UNIPROT IDs...)
Can anyone recommend me some program in order to obtain networks based on Gene Ontology?
Thank you very much in advance
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