[BioC] R: Pathway Information

Alexander C Cambon accamb01 at louisville.edu
Thu Jun 16 18:14:58 CEST 2005

Just correct the typo from "steriods" to "steroids" and it works.


>>> "Alberto Goldoni" <alberto.goldoni at eurogene.org> 6/16/2005 11:43 AM >>>
Sorry but it doesn't work:

> get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID),
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

>get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), sep
= ""), 

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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:
>### 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,
>### 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
>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.
>> Hi
>> Can anybody tell me the following
>> I want to identify genes which are located on a certain pathway NF
>> How can I obtain such an information. Which package is appropriate
>> which commands are needed. If any body ever encounterd the same
>> 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 

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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