Possibly a silly question...
I work on a non-model plant species that has a sequenced genome. All genes from the map were aligned against KEGG proteins, therefore about ~70% genes on the map are annotated with K-term.
I performed differential expression analyses and obtained a set of interesting genes (230 genes), and I have an input that looks something like this:
Gene_1 hsa:9380 K00049
Gene_3 mdo:100015233 K00081
Gene_4 ath:AT1G30270 K00924
Gene_5 ath:AT1G30270 K00924
Gene_6 ath:AT3G59420 K00924
Gene_7 ath:AT3G59420 K00924
where I have a gene name for my species, locus tag ID (and the species in which the best hit was identified with), and its corresponding K-term.
Now I wanted to do pathway enrichment analyses and get a p-value for enriched pathways, but having to pick a species to do so has been hindering the process. Does anyone know how to deal with a situation like this? Any help would be greatly appreciated.