I am currently working on a non-model plant species and after running interproscan, I realized that only a little over half (~38000 out of 63000 genes) get at least one GO term assigned to it. That way, if I were to do a GO enrichment analysis, some gene of interest (say, differentially expressed genes) may not have a GO term associated with it and, I suppose, that information would be lost in the enrichment analysis. So it GO enrichment analysis inherently biased/unreliable for non-model organism? If someone can point to some papers that discuss this that would be very helpful. If I were wrong, please correct me since I am new to this kind of analysis. Thanks in advance!