Hi,
Not sure if I have mis-understood. It looks like GAGE can be used for non-model organisms using KO?
I have a set of data - gene IDs with associated kegg Ids from using KAAS for my genome.
geneID           keggID
gene30651     K01416 ……...

I used this to match keggIDs with my set of differentially expressed genes I previously identified with their average fold change between control and treatment groups for each gene.
Is it possible to use this list of differentially expressed KEGG Ids to do pathway enrichment using GAGE and KO db?

geneID          keggID     FC
gene40167     k00236    43  …………….

Best wishes,

bekah

GAGE will work with your data if you:

-change the rowname of your data matrix or the names of your data vector to ko gene ID (keggID in your example)

-if the data is fold change already, set both ref and samp to NULL when calling gage function.

-follow/understand the tutorial and package documentation accurately

We have developed a web server for user with less programming skills, which can do both pathway/gage analysis and visualization:

https://pathview.uncc.edu/

HTHs,