Convert kegg ids to uniprot ids
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9.5 years ago
Anusha ▴ 10

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.

gene • 13k views
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9.5 years ago
Denise CS ★ 5.2k

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.

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Thanks a lot ! It worked.

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7.4 years ago
Lhl ▴ 760
  1. KEGG mapper convert ID http://www.genome.jp/kegg/tool/conv_id.html

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

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7.4 years ago
Lhl ▴ 760

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.

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7.4 years ago
Tonor ▴ 480

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

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