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
Quoting Auer Michael <michael.auer at="" meduniwien.ac.at="">:
> 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
KEGG and annaffy and annotation packages will have what you need.
and
> which commands are needed.
vignettes has all commands you need.
Saurin
> and
> which commands are needed. If any body ever encounterd the same
problem
> please let me know.
>
> Michael
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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
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
>Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is
authenticated by a
trusted mechanism)
>Received-SPF: none (hypatia: domain of rhaddad at genetics.wayne.edu
does not
designate permitted sender hosts)
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>Cc: bioconductor mailing list <bioconductor at="" stat.math.ethz.ch="">
>Subject: Re: [BioC] Pathway Information
>X-BeenThere: bioconductor at stat.math.ethz.ch
>X-Mailman-Version: 2.1.6
>List-Id: The Bioconductor Project Mailing List
<bioconductor.stat.math.ethz.ch>
>List-Unsubscribe:
<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">,
<mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe">
>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor="">
>List-Post: <mailto:bioconductor at="" stat.math.ethz.ch="">
>List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help">
>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">,
<mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe">
>Content-Transfer-Encoding: 7bit
>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on
pascal.dfci.harvard.edu
>X-Spam-Level:
>X-Spam-Status: No, score=-2.2 required=3.0 tests=AWL,BAYES_00
autolearn=ham
version=3.0.1
>
>
>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
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: gioved? 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
>Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is
authenticated by a
trusted mechanism)
>Received-SPF: none (hypatia: domain of rhaddad at genetics.wayne.edu
does
not
designate permitted sender hosts)
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>Cc: bioconductor mailing list <bioconductor at="" stat.math.ethz.ch="">
>Subject: Re: [BioC] Pathway Information
>X-BeenThere: bioconductor at stat.math.ethz.ch
>X-Mailman-Version: 2.1.6
>List-Id: The Bioconductor Project Mailing List
<bioconductor.stat.math.ethz.ch>
>List-Unsubscribe:
<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">,
<mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe">
>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor="">
>List-Post: <mailto:bioconductor at="" stat.math.ethz.ch="">
>List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help">
>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">,
<mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe">
>Content-Transfer-Encoding: 7bit
>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on
pascal.dfci.harvard.edu
>X-Spam-Level:
>X-Spam-Status: No, score=-2.2 required=3.0 tests=AWL,BAYES_00
autolearn=ham
version=3.0.1
>
>
>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
https://stat.ethz.ch/mailman/listinfo/bioconductor
Hi
Apologies to all for this being not strictly speaking BioC (although
the back
end does use some R/BioC functions to make heatmaps and the like)!
Have a look at:
http://www.madras.uwcm.ac.uk/
This is an Affy-focussed web-based environment where you can upload
and review
your data in a gene-centric fashion whilst also getting a biologist-
friendly
"executive summary" of what that gene does. It's free :-)
There is a public guest login option which gives you a few token
public datasets
to browse. If you go into Pathways you'll find we've dumped all the
BioCarta
pathways into it as well, including NFkappa B. Select this and you
get all the
genes on your affy chip from this pathway and browse away.
If anyone wants to discuss this with me in more detail (e.g. how to
get a login
or local install) then please contact me off-list.
Regards
David
Professor David Kipling
Department of Pathology,
School of Medicine,
Cardiff University,
Heath Park
Cardiff CF14 4XN
Email: KiplingD at cardiff.ac.uk
Tel: +44 29 2074 4847
fax: +44 29 2074 4276
>>> "Auer Michael" <michael.auer at="" meduniwien.ac.at=""> 06/16/05 10:24
AM >>>
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
_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Well, if so (regarding R and BioC in the back end, or other open
source
projects), it is considered collegial to state that on the front end
and
acknowledge the hard work of all the developers whose programs you are
using.
And please do read the posting guide, as this has nothing to do with
the
subject line.
Best wishes,
Robert
David Kipling wrote:
> Hi
>
> Apologies to all for this being not strictly speaking BioC (although
the back
> end does use some R/BioC functions to make heatmaps and the like)!
>
> Have a look at:
>
> http://www.madras.uwcm.ac.uk/
>
> This is an Affy-focussed web-based environment where you can upload
and review
> your data in a gene-centric fashion whilst also getting a biologist-
friendly
> "executive summary" of what that gene does. It's free :-)
>
> There is a public guest login option which gives you a few token
public datasets
> to browse. If you go into Pathways you'll find we've dumped all
the BioCarta
> pathways into it as well, including NFkappa B. Select this and you
get all the
> genes on your affy chip from this pathway and browse away.
>
> If anyone wants to discuss this with me in more detail (e.g. how to
get a login
> or local install) then please contact me off-list.
>
> Regards
>
> David
>
>
> Professor David Kipling
> Department of Pathology,
> School of Medicine,
> Cardiff University,
> Heath Park
> Cardiff CF14 4XN
>
> Email: KiplingD at cardiff.ac.uk
> Tel: +44 29 2074 4847
> fax: +44 29 2074 4276
>
>>>>"Auer Michael" <michael.auer at="" meduniwien.ac.at=""> 06/16/05 10:24
AM >>>
>
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>