Clusterprofiler for KEGG enrichment (non-model species)

Question

[sbchua.1990]

Hi, I wish to use clusterProfiler for KEGG pathway enrichment (non-model species, Pleurotus pulmonarius). I want to use my whole transcriptome as background. I now have files for whole transcriptome and DEG in the following format:

TRINITY_identifier KO_number

How can I proceed from here? What kind of extra input files are needed?

[Benn]

I am not sure for clusterProfiler in particular, but normally if you want to do KEGG or GO analysis with non-model species, you'll first need to know which genes of your mushroom map to which KEGG pathway or GO term. I don't think TRINITY identifiers are sufficient for this purpose.

[sbchua.1990]

Thanks for reply. Ko_number at second column. Do you have any suggestion for suitable software?

[Benn]

When I worked with non-model species, a decade ago, I used blast2go software for this. But I am not sure if this is still the best approach nowadays (and if it is still free software). I 've been working for too long with model species now.

Answer 1

[sutturka]

May be this document will be useful.