Map genes to KEGG pathways

Question

[joshf]

I have a list of ~13k genes that I need to map to KEGG pathways.

I’m aware that this has sort of been asked before but I’m not so sure the answers are still up-to-date? DAVID for example hasn’t been updated since 2010. Could I still use gene2pathway or subpathwayMiner without losing a lot of information? the latest versions of both were released about 5yrs ago so I’m unsure if I should..

Any advice appreciated

Answer 1

[Jean-Karim Heriche]

You can download all pathway assignments to genes with the REST API: http://rest.kegg.jp/link/pathway/hsa. The first column contains the Entrez gene ID (prefixed by hsa:) and the second column contains the pathway ID. You can also go gene by gene like so: http://rest.kegg.jp/link/pathway/hsa:11251 and you can get the pathway name with http://rest.kegg.jp/list/path:hsa04514.

[joshf]

I'll give this a try, thanks!

Answer 2

[EagleEye]

Gene Set Clustering based on Functional annotation (GeneSCF) - real-time based