This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Gene Symbol to KEGG

Hi!

I have a long list (R) which contains genes, compounds and other things (gex; glycan).

Example:

"CDK4" "C01245" "PIK3R5" "C05981" "C01245" "MAPK1" "E2F1"

I'm working with some pathways retrieved from KEGG and I want to know which elements from this list are genes and which are not.

I need to convert gene symbols to KEGG id, so far compounds and other that are not genes can be identified, because those are already in KEGG IDs.

names((keggGet("C00044"))[[1]]$ENTRY)

[1] "Compound"

names((keggGet("G13064"))[[1]]$ENTRY)

[1] "Glycan"

But this does not work with gene symbols.

names((keggGet("KRAS"))[[1]]$ENTRY)

Error in .getUrl(url, .flatFileParser) : Bad Request (HTTP 400).

I have tried using library(org.Hs.eg.db), but so far I have not been able to get the results that I expected.

Any hint?

Thanks for your time.

kegg symbol gene
• 14,249 views • link
updated by natasha.sernova natasha.sernova • written by Folder40g Folder40g

3 answers

You should convert the gene symbols to ENTREZ ids as they are not unique and then try to map them to the corresponding KEGG IDs Take a look at this answer here, this should serve the purpose for you.

• 1 views • link
written by ivivek_ngs ivivek_ngs

If the genes you are interested in are few you can use: http://rest.kegg.jp/find/genes/KRAS otherwise, you will save time by converting the gene symbol in ensembl/uniprot/entrez/ncbi id and then retrieve the pathway.

• 1 views • link
written by Girolamo Girolamo

See this post:

A: Ensembl ID to Gene Symbol

and this link inside:

https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

It may help you.

• 1 views • link
written by natasha.sernova natasha.sernova

Log in to answer this question.

More posts like this