Question: KEGG pathways associated to a gene using BiomaRt
3
gravatar for TitoPullo
5.3 years ago by
TitoPullo150
United Kingdom
TitoPullo150 wrote:

Hello,

is there an easy way to get the get the list of KEGG pathways associated to a specific gene using biomaRt?

I found a solution to retrieve the GO terms: How Do I Do Simple Go Term Lookup Given A Gene (Or Mrna) Identifier?.. Is it possible use something similar for KEGG pathway terms?

R kegg biomart pathways • 4.5k views
ADD COMMENTlink modified 4.8 years ago by sedaghat.nafiseh20 • written 5.3 years ago by TitoPullo150
3
gravatar for Martin Morgan
5.3 years ago by
Martin Morgan1.6k
United States
Martin Morgan1.6k wrote:

The REST service is also available from the KEGGREST R / Bioconductor package.

library(KEGGREST)
keggLink("pathway", "hsa:10327")  # pathways gene 10327 is in
p = keggLink("hsa", "pathway")
map = split(names(p), unname(p))  # gene -> pathway map

Queries follow closely the API provided by KEGG.

 

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Martin Morgan1.6k

Hi,

I tried this method to link gene to pathways. But there was an error: "arguments imply differing number of rows". Tried unsplit also. Can anyone tell, how to solve this error and view the 'map' file. 

ADD REPLYlink written 4.1 years ago by parvathi.sudha0
1
gravatar for Neilfws
5.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

I don't believe that KEGG is accessible through BioMart. However, you can use the TogoWS REST service to retrieve that information. Look at the examples in the KEGG GENES section on that page.

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Neilfws48k
0
gravatar for sedaghat.nafiseh
4.8 years ago by
United States
sedaghat.nafiseh20 wrote:

You can use 'graphite' R-package.

ADD COMMENTlink written 4.8 years ago by sedaghat.nafiseh20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2050 users visited in the last hour