Question: Gene Symbol to KEGG
0
gravatar for Folder40g
3.4 years ago by
Folder40g120
Folder40g120 wrote:

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.

symbol kegg gene • 3.5k views
ADD COMMENTlink modified 3.4 years ago by natasha.sernova3.6k • written 3.4 years ago by Folder40g120
0
gravatar for ivivek_ngs
3.4 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

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.

ADD COMMENTlink written 3.4 years ago by ivivek_ngs4.8k
0
gravatar for Girolamo
3.4 years ago by
Girolamo140
Italia
Girolamo140 wrote:

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.

ADD COMMENTlink written 3.4 years ago by Girolamo140
0
gravatar for natasha.sernova
3.4 years ago by
natasha.sernova3.6k
natasha.sernova3.6k wrote:

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.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by natasha.sernova3.6k
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: 993 users visited in the last hour