[BioC] R: R: Pathway Information

Sat Jun 18 09:01:12 CEST 2005

the other place to look for pathways is in the cMAP package - they are 
set up a bit differently, so you will need to do a bit more work (I 
think), but any reports on what did or did not work - to the list please 
- would be helpful. cMAP has both KEGG and BioCarta pathway data.

  Robert


Alberto Goldoni wrote:
> Now it works!
> 
> get(paste("hsa", get("Biosynthesis of steroids", KEGGPATHNAME2ID),sep=
> ""),KEGGPATHID2EXTID)
>  [1] "10654" "10682" "1717"  "1728"  "2222"  "2224"  "3156"  "3422"
> "4047"  "4597"  "4598"  "4835"  "51302" "6309"  "6713"  "79001" "91734"
> "9420"  "9453"
> 
> but if now i would like to create a file ex CVS in which i can have:
> 
> "10654" ----> pathway1.....
> "10682"-----> pathway2
> 
> 
> 
> "9420"------->pathwayN
> 
> how can i obtain it?
> 
> thanks
> 
> -----Messaggio originale-----
> Da: John Zhang [mailto:jzhang at jimmy.harvard.edu] 
> Inviato: giovedì 16 giugno 2005 17.56
> A: jzhang at jimmy.harvard.edu; michael.auer at meduniwien.ac.at;
> rhaddad at genetics.wayne.edu; alberto.goldoni at eurogene.org
> Cc: bioconductor at stat.math.ethz.ch
> Oggetto: Re: R: [BioC] Pathway Information
> 
> Sorry for the typo. steriods should be steroids.
> 
> 
>>X-Original-To: jzhang at jimmy.harvard.edu
>>Delivered-To: jzhang at jimmy.harvard.edu
>>From: "Alberto Goldoni" <alberto.goldoni at eurogene.org>
>>To: "'John Zhang'" <jzhang at jimmy.harvard.edu>,
> 
> <michael.auer at meduniwien.ac.at>, 
> <rhaddad at genetics.wayne.edu>
> 
>>Cc: <bioconductor at stat.math.ethz.ch>
>>Subject: R: [BioC] Pathway Information
>>Date: Thu, 16 Jun 2005 17:43:49 +0200
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>>Sorry but it doesn't work:
>>
>>
>>>get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID),
>>
>>sep= ""),KEGGPATHID2EXTID)
>>Error in get(x, envir, mode, inherits) : variable "Biosynthesis of
>>steriods" not find
>>
>>-----Messaggio originale-----
>>Da: bioconductor-bounces at stat.math.ethz.ch
>>[mailto:bioconductor-bounces at stat.math.ethz.ch] Per conto di John Zhang
>>Inviato: giovedì 16 giugno 2005 16.55
>>A: michael.auer at meduniwien.ac.at; rhaddad at genetics.wayne.edu
>>Cc: bioconductor at stat.math.ethz.ch
>>Oggetto: Re: [BioC] Pathway Information
>>
>>Suppose you are looking for gene that are involved in human
>>"Biosynthesis of 
>>steriods" pathway, the following will give you a vector of Entrez Gene
>>ids:
>>
>>
>>>library(KEGG)
>>>get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), sep
>>
>>= ""), 
>>KEGGPATHID2EXTID)
>>
>>
>>
>>>X-Original-To: jzhang at jimmy.harvard.edu
>>>Delivered-To: jzhang at jimmy.harvard.edu
>>>From: Ramsi Haddad <rhaddad at genetics.wayne.edu>
>>>To: michael.auer at meduniwien.ac.at
>>>Mime-Version: 1.0
>>>Date: 16 Jun 2005 09:58:13 -0400
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>>>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
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>>>Subject: Re: [BioC] Pathway Information
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>>>
>>>Dear Michael,
>>>	There is a pretty good description in the globaltest vignette.
>>
>>Most of
>>
>>>the stuff shown below is based on it:
>>>
>>>library(mgu74av2)
>>>library(KEGG)
>>>
>>>### this next line generates a list of kegg pathways and all
>>>### the probe sets that belong in a given pathway.
>>>mouse.kegg.sets <- as.list(mgu74av2PATH2PROBE)
>>>
>>>### the next 3 lines give the names of the pathways from their
>>>### kegg ID numbers
>>>all.kegg.ids <- ls(KEGGPATHID2NAME)
>>>all.kegg.names <- mget(all.kegg.ids, KEGGPATHID2NAME)
>>>table.of.keggs <- as.matrix(unlist(all.kegg.names))
>>>write.table(table.of.keggs, "keggs.csv", sep=",",col.names=NA,
>>>row.names=T)
>>>
>>>### here's how to get the name of a given kegg pathway:
>>>what.is.00010 <- get("00010", KEGGPATHID2NAME) ## this is glycolysis.
>>>
>>>### here's how to get the probesets in the Glycolysis Path from the
>>>mouse array:
>>>glycolysis.affyIDs <- get("00010", mgu74av2PATH2PROBE) ## there are 68
>>>such probe sets.
>>>another.glycolysis.affyIDs <- mouse.kegg.sets[["00010"]] ## more than
>>>one way to skin a cat
>>>
>>>### here's how to get the kegg pathway numbers for anything with
>>>"Cholera"
>>>colera.kegg.paths.index <- grep("Cholera", table.of.keggs) ## this
>>>provides the index
>>>colera.keggs <- table.of.keggs[colera.kegg.paths]
>>>### here it is in one step:
>>>### table.of.keggs[grep("Cholera", table.of.keggs)]
>>>
>>>hope that gets you started.
>>>
>>>Ramsi
>>>
>>>
>>>
>>>
>>>
>>>>Hi
>>>>
>>>>Can anybody tell me the following
>>>>
>>>>I want to identify genes which are located on a certain pathway NF
>>
>>Kappa.
>>
>>>>How can I obtain such an information. Which package is appropriate
>>
>>and
>>
>>>>which commands are needed. If any body ever encounterd the same
>>
>>problem
>>
>>>>please let me know.
>>>>
>>>>Michael
>>>
>>>-- 
>>>Ramsi Haddad, Ph.D.
>>>Center for Molecular Medicine and Genetics.
>>>Functional Genomics Laboratory,
>>>Perinatology Research Branch, NICHD, NIH.
>>>259 Mack Avenue,
>>>Room 3146 Applebaum Bldg.
>>>Detroit, MI 48201, USA.
>>>
>>>phone:(313) 577-2569 / fax:(313) 577-7736
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>Jianhua Zhang
>>Department of Medical Oncology
>>Dana-Farber Cancer Institute
>>44 Binney Street
>>Boston, MA 02115-6084
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
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>>
>>
> 
> 
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
> 
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