How to do gene enrichment with locally stored KEGG & Reactome data in R

Question

[patrickvanzalm]

Hi all,

For a collaboration project we are required to use R-studio in a remote environment. They have also provided the data from KEGG and Reactome on the same server, which we can access.

I'm used to just having my list of genes, and using packages such as enrichR, or string-db. I cant seem to figure out how to do similair enrichment analysis using locally stored pathway data.

The KEGG is stored in a single file:

• ko00001.keg

The REACTOME is stored in a few files:

• Complex_2_Pathway_human.txt
• Ewas2Pathway_human.txt
• ReactomePathways.txt
• ReactomePathwaysRelation.txt

Does anyone have experience running enrichment analysis using locally stored data? Or can anyone point me to R packages that could handle it?

Best,

Patrick

Answer 1

[Papyrus]

For example, the goseq package can be used with any custom file describing pathways/gene sets to perform enrichment analysis. (There is an example on section 6.6 of the user's guide, you can see what the input files look like and format your files in the same manner).

Answer 2

[EagleEye]

Here is one solution (but without R).

GO enrichment analysis using a Text file with all the genes and GO ids associated for a non model organism