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looking for a good pipeline for GO enrichment and network analysis of a non-model plant?
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GO enrichment analysis using non model organism
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You can use an approach mapping one-to-one orthologs with a well-annotated model organism, but you lose a lot of information on the many-to-one/one-to-many orthologs, or those genes unique to your non-model organism.
Alternatively, if you annotate your own annotations with GO terms, you can use a tools like g:Profiler2 which allows you provide your own custom dataset. Tutorial here.