[BioC] KEGG analysis

[Florian Hahne]

The tools in the gseaBase package are also pretty helpful for these  
kinds of problems.
Florian

On 06.04.2009, at 08:07, Daniel Brewer wrote:

> Just to answer my own question.  It seems that with a combination of  
> the
> annotation libraries "org.Hs.eg" and "KEGG", and a bit of scripting  
> you
> can do this sort of thing.
>
> Dan
>
> Daniel Brewer wrote:
>> Hello,
>>
>> I have two gene lists and I want to find out whether there are  
>> genes in
>> list one that occur in well known networks (KEGG?) where genes in  
>> list 2
>> also appear.
>>
>> For example,
>>
>> List 1: RAS, SPINK1
>> List 2: ERBB2
>>
>> Both RAS and ERBB2 occur in ERBB signalling pathway defined by KEGG.
>> SPINK1 does not appear in any common network (I think).
>>
>> Has anyone got any ideas what the best way to do this is?
>>
>> Many thanks
>>
>> Dan
>>
>>
>
> -- 
> **************************************************************
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
> Molecular Carcinogenesis
> Email: daniel.brewer at icr.ac.uk
> **************************************************************
>
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