How to get lists of genes for kegg pathways

Question

[valerie]

Hi!

Is it possible to get lists of genes for each of the existing kegg pathways? Like some kind of csv or xml file. Or maybe I can somehow get the pathways for each gene via python? I want to use the knowledge about kegg pathways for my genes in my program, but do not understand how to download this data.

Thanks!

[GenoMax]

While you may be able to get some of the data via KEGG REST interface you may violate their AUP if you try to download the entire KEGG data.

Answer 1

[Haci]

I can't offer a Python solution but here is some R code I have used in the past:

library(org.Hs.eg.db) # Genome wide annotation for Human

# org.Hs.egPATH contains Mappings between Entrez Gene identifiers and KEGG pathway identifiers
kegg_paths <- as.list(org.Hs.egPATH2EG)

kegg_path is a list, in which each element is a human kegg pathway. For each of these elements, kegg identifiers are used as "names". You can convert this R list to a Python dictionary using an intermediate JSON file; rpy2 is another option to do so.

[valerie]

Haci, thank you! Could you please also tell me how to get the information about corresponding pathway and gene names for the id's?