Question: How to get lists of genes for kegg pathways
1
gravatar for valerie
4 months ago by
valerie80
valerie80 wrote:

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!

kegg gene • 184 views
ADD COMMENTlink modified 4 months ago by Haci330 • written 4 months ago by valerie80

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.

ADD REPLYlink written 4 months ago by genomax80k
1
gravatar for Haci
4 months ago by
Haci330
Haci330 wrote:

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.

ADD COMMENTlink written 4 months ago by Haci330

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

ADD REPLYlink written 4 months ago by valerie80
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