GO in Bioconductor
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John Zhang ★ 2.9k
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> How can I use Gene Ontology in BioC? Is there any tutorial or manual available? Especially how can I construct (extract) a tree if I have a gene name (e.g. RAD52) GO() lists all the environments of the GO package. ?environment name gives you the description of the environment of interest with some example code. For the thing you would like to do you may try to get the Gene id for the gene (e. g. 19365) and then do the following: > goids <- get("19365", GOLOCUSID2GO) You will get a few goids the gene maps to. Suppose we are interested in GO:0005515 that belongs to MF. > get("GO:0005515", GOMFPARENTS) # Get the direct parents > get("GO:0005515", GOMFCHILDREN) # Get the direct children > get("GO:0005515", GOMFANCESTOR) # Get the parents and grand parents ... > get("GO:0005515", GOMFOFFSPRING) # Get the children and grand children ... The above do not give you enough to construct a GO tree but you can always search the Gene Ontology web site for a tree. > > Thanks and regards, > Kaustubh > > > >--------------------------------- > > Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever. > [[alternative HTML version deleted]] > >_______________________________________________ >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
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Hi, For any chip, you can get it using the purpose built environments. For generic gene names, either biomaRt or some site such as NCBI can be used. But in general there are multiple GO ids for any gene (and you need to be a bit more careful in describing what you want - only the most specific GO terms or all GO terms - either are available in the meta-data packages, from other sources, you would need to get the most specific terms [generally that is what they give] and then build the GO graph. This can be done using tools in GOstats. The vignette there should be self-explanatory, if not please let me know (on this list) what problems you encounter, best wishes Robert Kaustubh Patil wrote: > Dear John, > > Thank you very much for your reply. I would like to know, how to get GOID from gene name? Is it possible using BioC or I have to do it explicitely? > > Regards, > Kaustubh > > John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > >>How can I use Gene Ontology in BioC? Is there any tutorial or manual > > available? Especially how can I construct (extract) a tree if I have a gene name > (e.g. RAD52) > > GO() lists all the environments of the GO package. > ?environment name gives you the description of the environment of interest with > some example code. > > For the thing you would like to do you may try to get the Gene id for the gene > (e. g. 19365) and then do the following: > > >>goids <- get("19365", GOLOCUSID2GO) > > > You will get a few goids the gene maps to. Suppose we are interested in > GO:0005515 that belongs to MF. > > >>get("GO:0005515", GOMFPARENTS) # Get the direct parents >>get("GO:0005515", GOMFCHILDREN) # Get the direct children >>get("GO:0005515", GOMFANCESTOR) # Get the parents and grand parents ... >>get("GO:0005515", GOMFOFFSPRING) # Get the children and grand children ... > > > The above do not give you enough to construct a GO tree but you can always > search the Gene Ontology web site for a tree. > > > > >>Thanks and regards, >>Kaustubh >> >> >> >>--------------------------------- >> >>Ring in the New Year with Photo Calendars. Add photos, events, holidays, > > whatever. > >>[[alternative HTML version deleted]] >> >>_______________________________________________ >>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 > > > > > > --------------------------------- > > Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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John Zhang ★ 2.9k
@john-zhang-6
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> Thank you very much for your reply. I would like to know, how to get GOID from gene name? Is it possible using BioC or I have to do it explicitely? I would get it from NCBI. > > Regards, > Kaustubh > >John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: >> How can I use Gene Ontology in BioC? Is there any tutorial or manual >available? Especially how can I construct (extract) a tree if I have a gene name >(e.g. RAD52) > >GO() lists all the environments of the GO package. >?environment name gives you the description of the environment of interest with >some example code. > >For the thing you would like to do you may try to get the Gene id for the gene >(e. g. 19365) and then do the following: > >> goids <- get("19365", GOLOCUSID2GO) > >You will get a few goids the gene maps to. Suppose we are interested in >GO:0005515 that belongs to MF. > >> get("GO:0005515", GOMFPARENTS) # Get the direct parents >> get("GO:0005515", GOMFCHILDREN) # Get the direct children >> get("GO:0005515", GOMFANCESTOR) # Get the parents and grand parents ... >> get("GO:0005515", GOMFOFFSPRING) # Get the children and grand children ... > >The above do not give you enough to construct a GO tree but you can always >search the Gene Ontology web site for a tree. > > > >> >> Thanks and regards, >> Kaustubh >> >> >> >>--------------------------------- >> >> Ring in the New Year with Photo Calendars. Add photos, events, holidays, >whatever. >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>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 > > > > > >--------------------------------- >Yahoo! Photos > Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever. Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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Hi Kaustubh, If you are using specific gene chips that BioC builds the annotation package for them, you can do the following instead of going to NCBI website. For example, if you are using Affymetrix Human Genome U95 Set Gene Chip, the annotation package hgu95av2 is designed for it. Suppose that you are interested in the GOID of the following gene names: "tubulin, beta 3", "POU domain, class 2, transcription factor 2", and "BTG family, member 2". Then first you have to figure out which probe set ids in this chip are associated with these three gene names. Do the following: library(hgu95av2) geneName <- c("tubulin, beta 3", "POU domain, class 2, transcription factor 2", "BTG family, member 2") geneNameAll <- unlist(as.list(hgu95av2GENENAME)) geneIndex <- match(geneName, geneNameAll) probeSetIds <-names(geneNameAll[geneIndex]) Then the next step is to find out the GOIDs for these probeSetIds by using hgu95av2GO: mget(probeSetIds, hgu95av2GO) If you are not using specific gene chip with annotation package available, you have to get the GOIDs from NCBI website as John suggested. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Thu, 5 Jan 2006, John Zhang wrote: > > > Thank you very much for your reply. I would like to know, how to get GOID from > gene name? Is it possible using BioC or I have to do it explicitely? > > I would get it from NCBI. > > > > > Regards, > > Kaustubh > > > >John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > >> How can I use Gene Ontology in BioC? Is there any tutorial or manual > >available? Especially how can I construct (extract) a tree if I have a gene > name > >(e.g. RAD52) > > > >GO() lists all the environments of the GO package. > >?environment name gives you the description of the environment of interest with > >some example code. > > > >For the thing you would like to do you may try to get the Gene id for the gene > >(e. g. 19365) and then do the following: > > > >> goids <- get("19365", GOLOCUSID2GO) > > > >You will get a few goids the gene maps to. Suppose we are interested in > >GO:0005515 that belongs to MF. > > > >> get("GO:0005515", GOMFPARENTS) # Get the direct parents > >> get("GO:0005515", GOMFCHILDREN) # Get the direct children > >> get("GO:0005515", GOMFANCESTOR) # Get the parents and grand parents ... > >> get("GO:0005515", GOMFOFFSPRING) # Get the children and grand children ... > > > >The above do not give you enough to construct a GO tree but you can always > >search the Gene Ontology web site for a tree. > > > > > > > >> > >> Thanks and regards, > >> Kaustubh > >> > >> > >> > >>--------------------------------- > >> > >> Ring in the New Year with Photo Calendars. Add photos, events, holidays, > >whatever. > >> [[alternative HTML version deleted]] > >> > >>_______________________________________________ > >>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 > > > > > > > > > > > >--------------------------------- > >Yahoo! Photos > > Ring in the New Year with Photo Calendars. Add photos, events, holidays, > whatever. > 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 >
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