Hi, Could you give us a list of 10 unmatched? BR viritha kaza wrote: > Hi > thanks for the reply: > As samuel suggested I used the following link > ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.xrefs.gz. > For the once I didnot find,I used the following code > > Though I still dont get 1:1 mapping, I got the entrez and the gene > symbol.The ipi_test file contains the list of IPI that I want to convert. > > code: > >source('http://bioconductor.org/biocLite.R') > > biocLite("biomaRt") > >library("biomaRt") > >ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > >ipi=scan("ipi_test.txt",what =character(),sep='\n',quote="") > >getBM(attributes = > c("ipi","entrezgene","hgnc_symbol"),filters="ipi",values=ipi,mart = > ensembl) > >write.table(ipi_entrez,"ipi_entrez_test.txt",sep='\t') > > I am still not getting a few.Is there any other method or should I > think that those IPI numbers dont have corresponding gene symbols? > Thanks, > Viritha -- Samuel GRANJEAUD granjeau at tagc.univ-mrs.fr INSERM - ICIM - TAGC Tel: +33 (0)491 82 87 11/24 http://tagc.univ-mrs.fr Fax: +33 (0)491 82 87 01 http://icim.marseille.inserm.fr/proteomique

Hi Viritha, These things can never be 1:1, but you can pretty easily just cram them all into a huge data.frame by doing this: library(org.Hs.eg.db) allAnnots <- merge(toTable(org.Hs.egPROSITE), toTable(org.Hs.egGO), by.x="gene_id", by.y="gene_id") head(allAnnots) Once you have done this, you may notice that they are not only are these things almost never (if ever) 1:1, but that this could have been even worse if I had used the GO2ALL mappings (and I probably should have, but I can't really tell because I have almost no information about what you want to do). Anyhow, I hope this helps you, but if you have a more specific use for this information that you are willing to talk about then we might be able to give you a better answer. Marc ----- Original Message ----- From: "viritha kaza" <viritha.k@gmail.com> To: "Manca Marco (PATH)" <m.manca at="" maastrichtuniversity.nl=""> Cc: bioconductor at stat.math.ethz.ch Sent: Thursday, February 17, 2011 9:46:28 AM Subject: Re: [BioC] IPI to entrez id Hi thanks for the reply: As samuel suggested I used the following link ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.xrefs.gz. For the once I didnot find,I used the following code Though I still dont get 1:1 mapping, I got the entrez and the gene symbol.The ipi_test file contains the list of IPI that I want to convert. code: >source('http://bioconductor.org/biocLite.R') > biocLite("biomaRt") >library("biomaRt") >ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >ipi=scan("ipi_test.txt",what =character(),sep='\n',quote="") >getBM(attributes = c("ipi","entrezgene","hgnc_symbol"),filters="ipi",values=ipi,mart = ensembl) >write.table(ipi_entrez,"ipi_entrez_test.txt",sep='\t') I am still not getting a few.Is there any other method or should I think that those IPI numbers dont have corresponding gene symbols? Thanks, Viritha On Wed, Feb 16, 2011 at 12:23 PM, Manca Marco (PATH) < m.manca at maastrichtuniversity.nl> wrote: > > > Hi Viritha, > > I have found this old answer to a similar question and I think it should > still apply: > > << > > Not sure that it is this easy. The IPI are protein identifiers. GO > categories classify genes. Neither the mapping from protein to gene or > gene to GO category is 1:1. GO categories form a hierarchy. So there are > significant decisions to be made in representing IPI identifiers in a > pie chart of GO terms. > > Bioconductor maintains 'org' and 'GO' database packages that provide the > necessary link between IPI protein ids and GO gene ontology categories, > via ENTREZ gene ids. Code might look like > > ## once only, to install packages > source('http://bioconductor.org/biocLite.R') > biocLite('org.Hs.eg.db', 'GO.db') > > ## from IPI to ENTREZ id, not 1:1 > library(org.Hs.eg.db) > ipi2eg = revmap(eapply(org.Hs.eg.db, names)) ## NOT 1:1 map > > ## Assume ipiIds is, e.g., c('IPI00008860', 'IPI00019922') > egIds = revmap(ipi2eg[ipiIds]) > > ## get GO terms, also not 1:1 > goIds = eapply(org.Hs.egGO[names(egIds)], names) > > You're still left with the problem of resolving multiple mappings and > the hierarchical relationship between GO terms. > > Martin > > >> > > > All the best, Marco > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology > - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX > Maastricht > > E-mail: m.manca at maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > > ******************************************************************** ************************************************* > > This email and any files transmitted with it are confidential and solely > for the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. > If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received > this email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on > +31626441205 Dr Marco MANCA > > > ******************************************************************** ************************************************* > ________________________________________ > Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] > per conto di viritha kaza [viritha.k at gmail.com] > Inviato: mercoled? 16 febbraio 2011 18.15 > A: Bioconductor > Oggetto: [BioC] IPI to entrez id > > Hi group, > I would like to convert a list of 3000 IPI's to genesymbol and entrez id. > eg : * * *IPI00658210 *to 57599, WDR48. > I wanted a 1:1 mapping. > Could anyone suggest the function and the package which could help me in > the > process. > Thank u in advance, > Viritha > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor