Question: Convert kegg ids to uniprot ids
0
gravatar for Anusha
4.4 years ago by
Anusha0
United States
Anusha0 wrote:

I have a set of genes with KEGG ids and I want their respective uniprot ids. Ho w can I do that? Or is there any possibility of getting a list of genes that are involved in a pathway with their uniprot ids For example, I need uniprot IDs of all the genes that are involved in Hippo signaling pathway.

tutorial gene • 5.5k views
ADD COMMENTlink modified 2.3 years ago by Tonor420 • written 4.4 years ago by Anusha0
4
gravatar for Denise - Open Targets
4.4 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.8k wrote:

In the UniProtKB page there is a tool to make that conversion for you. I can see the KEGG is in their list...You can also use BioMart Central: under 'Interactions and pathways' click on Reactome and under filters choose KEGG IDs. If you are not too familiar with BioMart, it is a data retrieval tool (online version but programmatic access too) that goes through four steps: data, filters, attributes and results. There is an youtube tutorial video showing how to go through those steps using the Ensembl BioMart. It should be similar when using Reactome BioMart.

ADD COMMENTlink written 4.4 years ago by Denise - Open Targets4.8k

Thanks a lot ! It worked.

ADD REPLYlink written 4.4 years ago by Anusha0
2
gravatar for Lhl
2.3 years ago by
Lhl730
United States
Lhl730 wrote:
  1. KEGG mapper convert ID http://www.genome.jp/kegg/tool/conv_id.html

  2. uniprot Retrieve/ID mapping www.uniprot.org/uploadlists

ADD COMMENTlink written 2.3 years ago by Lhl730
1
gravatar for Guangchuang Yu
2.3 years ago by
Guangchuang Yu2.1k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.1k wrote:

using clusterProfiler:

https://guangchuangyu.github.io/2016/05/convert-biological-id-with-kegg-api-using-clusterprofiler/

ADD COMMENTlink written 2.3 years ago by Guangchuang Yu2.1k
0
gravatar for Lhl
2.3 years ago by
Lhl730
United States
Lhl730 wrote:

If you want to do this locally, you can download idmapping file form Uniprot ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/. Then with some simple awk/grep unix commands or a couple of python/perl scripts, you will be able to extract uniprot id(s) of the correspondent kegg id and vice versa.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Lhl730
0
gravatar for Tonor
2.3 years ago by
Tonor420
UK
Tonor420 wrote:

DAVID (Database for Annotation, Visualization and Integrated Discovery) has a Gene ID Conversion Tool: https://david.ncifcrf.gov/conversion.jsp

ADD COMMENTlink written 2.3 years ago by Tonor420
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