Hi
How i can get the list of genes for each KEGG pathways ? I need a simple text table that in each row i have the KEGG pathway and next column has the list of genes for this specific pathway.
Best
Malik
A not up-to-date list can be accessed in R through the annotation library
org.Hs.eg.db (human) and org.Mm.eg.db (mouse). With as.list(org.Hs.egPATH2EG) you will get a list of all pathways (itmes names are KEGG pathway IDs and each item is a vector of NCBI gene IDs that are assigned to the respective pathway). You can save this as a text file in the format you want, e.g. with
library(org.Hs.eg.db)
mapped
Your question is relevant. Kegg is owned by 2 Japan companies. You can ask this question by e-mail to:
They are nice to answer in a couple of days. Please frame your question in a clear way to them.
A not up-to-date list can be accessed in R through the annotation library
org.Hs.eg.db (human) and org.Mm.eg.db (mouse). With as.list(org.Hs.egPATH2EG) you will get a list of all pathways (itmes names are KEGG pathway IDs and each item is a vector of NCBI gene IDs that are assigned to the respective pathway). You can save this as a text file in the format you want, e.g. with
library(org.Hs.eg.db)
mapped
Hi malik, if you use R, then an updated list can be obtained using the Gage package. Check the yr pretty nice and complete documentsrion to know the how to https://bioconductor.org/packages/release/bioc/html/gage.html. You will get the information in list objects if you need help dealing with list just let me know...
Best,
mar
@Mar, I think using KEGGREST directly would be better rather than via another package (like gage, for instance). I am not sure if there are licencing issues and what version of KEGG data can be accessed (would be happy if someone tells me!).
@Jochen, this is what the gage manual say "another advantage of using kegg.gsets is that you get the most updated pathway gene set data as it is retrieved from KEGG in real time..." Page 4 in https://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf.
But will be interesting to confirm it by comparing the results with KEGGREST as you suggest. I will do it next time I need to do pathways analysis. Thanks for the tip!
You might check it as well, the function is quite simple to understand and have some extra option
Search KEGG Pathway Maps by Keyword in R
https://biobeat.wordpress.com/category/r/
you can download list of pathway an the genes for humans http://rest.kegg.jp/link/hsa/pathway .
You can use excel or sql or any language of your choice, to group the list based on unique pathway and a grouped comma or space separated list of genes. If this is what you need can make that file and share.
Hi Malik,
You can find the lists here Broad Institute:
http://software.broadinstitute.org/gsea/downloads.jsp
Archived versions are also accessible.
Best,
Cigdem
@ Malik Yousef
@ Cigdem,
Do you have any info as to when the lists of genes in KEGGS/GO were last updated on http://software.broadinstitute.org/gsea/downloads.jsp?
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