[BioC] Gene symbol to KEGG gene ids

[Daniel Brewer]

Hi Marc,

Many thanks for that.  The process you describe gives you the pathway
KEGG ID rather than the KEGG gene ID.  This information is currently not
available in the org.Hs.eg.db package.  I have manage to get a
satisfactory solution from other replies.

Thanks for your time and the interesting insight.

Dan

Marc Carlson wrote:
> Hi Daniel,
> 
> To get get the KEGG IDs associated with a particular gene symbol you
> must first convert the gene symbols from the org.Hs.eg.db package into
> Entrez Gene IDs.  There are two reasons for this.  The 1st is that we
> never want to use gene symbols as primary identifiers because they are
> not unique.  And the 2nd reason is because the org.Hs.eg.db package is
> Entrez Gene centric.  So if you have an Entrez Gene ID, then you can get
> to every other piece of information in the org.Hs.eg.db package database. 
> 
> To achieve this we can do the following: 
> 
> library(org.Hs.eg.db)
> 
> ##Toy example symbols:
> sym = c("AKT3","CDH1")
> 
> ##Get the Entrez gene IDs associated with those symbols
> EG_IDs = mget(sym, revmap(org.Hs.egSYMBOL),ifnotfound=NA)
> 
> ##Then get the KEGG IDs associated with those entrez genes.
> KEGG_IDs = mget(as.character(EG_IDs), org.Hs.egPATH,ifnotfound=NA)
> 
> 
> Please let me know if you have more questions.
> 
> 
>   Marc
> 
> 
> 
> 
> Daniel Brewer wrote:
>> Hello,
>>
>> The org.Hs.eg.db package provides annotations that link a gene to a
>> particular KEGG pathway.  What I would like to know is what is what are
>> the KEGG ids associated with this gene symbol.  This information does
>> not seem to be available in either KEGG.db or org.Hs.eg.db, but must be
>> used to construct the annotation files.  Does anyone know how to get
>> this info?
>>
>> Thanks
>>
>> Dan
>>
>>   
> 

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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