Kegg annotation for gene

Question

[ehruan]

Hi, is there a package in R or python that I can use to find the pathways associated to a gene if I input a list of genes? I have tried using KEGG search mapper but I have a list of a thousand genes or so and need the pathways for each gene so this is not my most ideal method. I am not trying to do any analysis, I just want to know the pathways a gene is in. An example output I am thinking is each individual gene with a list of the pathways associated with it. Thank you!

[GenoMax]

Take a look at GeneSCF (LINK). There should be past posts by the author of GeneSCF to find this information from KEGG.

Answer 1

[pfchuckran]

I've used the KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) to download lists of KO numbers for each module, pathway, and enzyme. So for pathways it would be: http://rest.kegg.jp/link/ko/path

These lists don’t have the pathway names, but you can also access them like this: http://rest.kegg.jp/list/path

You would just have to join them after that!

Alternatively there is the package KeggRest. But it might be more than what you need at the moment

Answer 2

[xanderpico]

As an alternative to KEGG, the rWikiPathways package in Bioconductor makes this easy: https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html. Once you've installed the package, then you can search by gene symbols (e.g., HGCN symbols) such "TNF" and get a dataframe listing pathways by row:

findPathwaysByXref('TNF','H')

You can alternatively search by NCBI Entrez Gene IDs or Ensembl IDs, etc. See examples and link to datasource codes in the man page:

?findPathwayIdsByXref