GO terms annotation file format to use in PANTHER

Question

[ishengomae]

I am getting started in the whole exercise so I'm a bit in the learning process. I have a list of about 100 genes identified with ensembl transcript ids (eg. ENSBTATXXXXXX for a given bovine transcript). I want to annotate these gene with GO terms, do some gene set enrichment analysis and identify perturbed pathways. The genes were identified by a positive selection scan through some thousands of background genes. Which tool would do a better job? I learn that PANTHER can do but just don't know which file format the inputs should be, so really I would appreciate if somebody can recommend to me an easy to use tool with good procedural documentation.

Thanks.