Good morning to everyone,
I'd like to perform a KEGG Pathway Enrichment analysis on my target organism (Eggplant - Solanum melongena). Unfortunately, the genome of reference is not avaliable among KEGG organisms... so I can't really use any default KEGG-designed package to retrieve KEGG Pathway terms from KO ones...
I tried to annotate the genome myself with KAAS, but (maybe I'm missing something) I only get KO terms. Instead, I'd like to carry out a KEGG pathway analysis, in a similar way I did with topGO, with its KEGG counterpart topKEGG and obtain similar plots (like the picture at the end of my post). I'd like to use KEGG Pathway terms, not KO ones.
So, basically:
- How do I get a KEGG Pathway annotation? KAAS apparently only gives me KO terms. And automatic retrieving from reference organisms on KEGG official databases apparently isn't an option because eggplant isnt' annotated.
-What package would you suggest? Again, I can't use default ones, but I can provide external annotation once I understand how to get KEGG Pathway Terms. I could either run a kegga (downstream edgeR) analysis, also on the basis of gene expression, or perform an enrichment through topKEGG, which also includes bar plots.
Any suggestions?
Thank you in advance.
