Convert kegg ids to uniprot ids

Question

[Anusha]

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.

Answer 1

[Denise CS]

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.

[Anusha]

Thanks a lot ! It worked.

Answer 2

[Lhl]

1. KEGG mapper convert ID http://www.genome.jp/kegg/tool/conv_id.html

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

Answer 3

[Guangchuang Yu]

using clusterProfiler:

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

Answer 4

[Lhl]

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.

Answer 5

[Tonor]

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