Question: How to get list of GeneIDs using SNP ID list?
1
gravatar for goksoy66
4.8 years ago by
goksoy6650
Turkey
goksoy6650 wrote:

Is there any way to get the list of gene IDs by giving SNP IDs, via a web (REST) service? I need services like following:

http://www.kegg.jp/kegg/docs/keggapi.html

I have a SNP list (like rs1312321, rs4524523), and I need to find the mapping gene list of these SNPs. Then I will search for KEGG pathways having these gene IDs. 

SNP List --> Gene List --> Pathway List 

snp kegg dbsnp pathway gene • 2.7k views
ADD COMMENTlink modified 4.8 years ago by Maxime Lamontagne2.1k • written 4.8 years ago by goksoy6650
2
gravatar for Emily_Ensembl
4.8 years ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

You can use the Ensembl VEP.

ADD COMMENTlink written 4.8 years ago by Emily_Ensembl19k
2
gravatar for goksoy66
4.8 years ago by
goksoy6650
Turkey
goksoy6650 wrote:

thanks for answer.

now I can get gene ids, but they are in type of Ensembl Gene ID. So I need to convert them to KEGG Gene ID.

KEGG REST API allows conversion from ncbi-gi, ncbi-geneid and uniprot. So these types are also ok for me. I can convert them using following rest url.

http://rest.kegg.jp/conv/genes/ncbi-geneid:3113320

Do you know a way to convert from ENSG to other ids?

 

ADD COMMENTlink written 4.8 years ago by goksoy6650
1

You can get Uniprot IDs as VEP output. Just open up the Identifiers and frequency data menu and select Uniprot.

ADD REPLYlink written 4.8 years ago by Emily_Ensembl19k
1

I couldn't find any web service. Here we can query via graphical user interface, only. 

ADD REPLYlink written 4.8 years ago by goksoy6650
1

Really? The link I sent you has a big blue button that says Launch VEP.

ADD REPLYlink written 4.8 years ago by Emily_Ensembl19k
1

Really? Did you understand what I mean? I want to convert IDs programmatically. So I need a rest service like this.

http://rest.kegg.jp/conv/genes/ncbi-geneid:3113320

If we click to that big blue button, we only get a GUI. 

ADD REPLYlink written 4.8 years ago by goksoy6650
1

Yes, you said you wanted a GUI, so I pointed you to a GUI. If you want a REST service then click on the big white button that says REST.

ADD REPLYlink written 4.8 years ago by Emily_Ensembl19k
1

You can try this one:

http://idconverter.bioinfo.cnio.es/

 

And if you want to try in my way, you just have to tweak these files:

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by EagleEye6.4k
2
gravatar for EagleEye
4.8 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/

'variant_summary.txt.gz' file has all clinical variants mapped to Genes (Column4:GeneID, Column5: GeneSymbol and Column7: rsID)

 

ADD COMMENTlink written 4.8 years ago by EagleEye6.4k
1
gravatar for Maxime Lamontagne
4.8 years ago by
Québec
Maxime Lamontagne2.1k wrote:

SNPnexus (http://www.snp-nexus.org/)

 

ADD COMMENTlink written 4.8 years ago by Maxime Lamontagne2.1k
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