[BioC] pathway analysis package

[Saurin D. Jani]

Hi,

Regarding Pathway analysis: 

In bioconductor when I load: library(KEGG)

I can do this:
kegg <- as.list(rae230aPATH2PROBE);

and I can generate heatmap of pathway probes which are involved in my DEgenes
so, I can see which genes are up and down in perticular pathway.

how can I use interaction data extracted from human BioCarta pathways for my
differentially expressed genes?

if anyone has done please let me know...


Thank you,
Saurin


-- 
|------------------------------------------------
| Saurin Jani
| Bioinformatician
|
| Department of Cell Biology and Anatomy
| Medical  University of South Carolina (MUSC)
| 173 Ashley Ave
| Charleston,SC - 29407 (US)
| 
| Email: jani at musc.edu
| Phone: (843)792-5483
|------------------------------------------------



Quoting Robert Gentleman <rgentlem at fhcrc.org>:

> There is a KEGG package, and we also have KEGGSOAP that give you access  
> to the KEGG data (for non-commercial use, if I recall correctly). You  
> can supplement this with the graph package, RBGL and Rgraphviz to do  
> most of the pathway stuff you want to.
> 
>   Another option is to make use of the CMAP data, which is potentially  
> more interesting because it has the pathways already represented as a  
> graph. But it is also more work as we have not managed to build any  
> interfaces for this (they have some though);
>    the url is http://cmap.nci.nih.gov/PW
> 
>   Robert
> 
> On Dec 16, 2004, at 3:11 PM, Josephine Liang wrote:
> 
> > Hi, fellow bioconductor members;
> >
> > In my memory, there is a vague rememberance that this is a package in  
> > Bioconductor called Pathway, I went to Bioconductor site , could not  
> > find a package named pathway in release 1.5, did I remember it wrong?  
> > Or the package is in an older release?  If it is, which release it is?  
> >  how do I access it?
> >
> > Thanks for all your help in advance
> >
> > Josephine
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> >
> +----------------------------------------------------------------------- 
> ----------------+
> | Robert Gentleman              phone: (206) 667-7700                    
>           |
> | Head, Program in Computational Biology   fax:  (206) 667-1319   |
> | Division of Public Health Sciences       office: M2-B865               
>        |
> | Fred Hutchinson Cancer Research Center                                 
>           |
> | email: rgentlem at fhcrc.org                                              
>                           |
> +----------------------------------------------------------------------- 
> ----------------+
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>