How to view all KEGG reactions?

Question

[Trombone Engineer]

I would like to assemble a network connecting some genomic data based on metabolism and KEGG reaction IDs. Is there a way that I can view all reactions listed on the KEGG database?

Answer 1

[Lluís R.]

You can have a look at the KEGG.db package at Bioconductor. But there isn't free (updated) access to the whole database see here)

Answer 2

[alserg]

You can get up-to-date links between kegg reaction IDs and genes using KEGG REST API. You can first find mapping from reactions to enzymes and then from enzymes to human genes:

library(KEGGREST)
rxn2enz <- keggLink("enzyme", "reaction")
enz2hsa <- keggLink("hsa", "enzyme")

Replace hsa with the organism code you need.

[superdanny68]

Hi, now that I've done linking enzymes to reactions and a chosen gene to enzyme, how do I view which reactions are associated with the chosen gene? Thanks

[alserg]

For example, like this:

rxnrnz <- data.frame(rxn=names(rxn2enz), enz=rxn2enz)
rxn2enz <- data.frame(rxn=names(rxn2enz), enz=rxn2enz)
enz2hsa <- data.frame(enz=names(enz2hsa), hsa=enz2hsa)

[superdanny68]

Got it! Thanks for answering.

Answer 3

[EagleEye]

Check if this helps,

http://rest.kegg.jp/list/reaction

Example for batch retrieval:

A: Retriving compounds name from KEGG IDs

Answer 4

[Trombone Engineer]

For anyone who might look this up, I did actually find this information within KEGG's website. The URL http://www.genome.jp/kegg-bin/get_htext?br08201.keg, which is available from the webpage http://www.genome.jp/kegg/brite.html and listed on the link for "Enzymatic reactions" shows all of the reaction information I had been looking for. This includes compound names, reaction IDs, and hierarchies. Other links from the same BRITE URL above have a conversion list of KO terms to reaction IDs and multiple other full listings that I was able to carry out network analysis around.