Hi list, Please forgive if this was asked before. In R, is there a way to find out how many Human gene products in a GO term (including all its children) like those reported in AmiGo? I'm talking about ALL the gene products, not just those on a affy chip. For example, for GO:0005921 and children and its children, the number is 6. Many thanks! ...Tao

Hi Tao, Shi, Tao wrote: > Hi list, > > Please forgive if this was asked before. > > In R, is there a way to find out how many Human gene products in a GO > term (including all its children) like those reported in AmiGo? I'm > talking about ALL the gene products, not just those on a affy chip. > For example, for GO:0005921 and children and its children, the number > is 6. There are only 6 if you restrict to TAS and IDA. If you allow IEA then there are 27: > library(org.Hs.eg.db) > get("GO:0005921", org.Hs.egGO2ALLEGS) TAS TAS IEA IEA IEA TAS "1823" "2697" "2700" "2701" "2702" "2703" TAS TAS IEA IEA IEA IEA "2705" "2706" "2707" "2709" "4284" "9742" IEA IEA IEA IEA IEA IEA "10052" "10804" "24145" "56666" "57165" "57369" IEA IEA IEA IDA IEA IEA "81025" "84694" "116337" "125111" "127534" "219770" IEA IEA IEA "349149" "375519" "100126572" Best, Jim > > Many thanks! > > ...Tao > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662

Well, you have to decide which database you believe! For example, if you think Ensembl is correct, then use biomaRt -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Shi, Tao Sent: 01 October 2008 01:43 To: bioconductor at stat.math.ethz.ch Subject: [BioC] gene count in a GO term Hi list, Please forgive if this was asked before. In R, is there a way to find out how many Human gene products in a GO term (including all its children) like those reported in AmiGo? I'm talking about ALL the gene products, not just those on a affy chip. For example, for GO:0005921 and children and its children, the number is 6. Many thanks! ...Tao _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Thanks, Jim and Michael, for the speedy replies! Following up Michael's point, I tried biomaRt, but the number of genes seems way too low comparing what reported on geneontology webpage (see below). I'm not sure how they're mapped. "org.Hs.eg.db" gave comparable number, which is not surprising as it derived directly from the gene ontology site. ###=================================================================== == ## GO:0005575 is the root term for CC, there are 9428 gene product according to AmiGo ##==================================================================== == > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok > tmp <- getBM(attributes=c( "ensembl_gene_id"), filters="go",values="GO:0005575", mart = mart) > dim(tmp) [1] 641 1 > tmp <- getBM(attributes=c( "entrezgene"), filters="go",values="GO:0005575", mart = mart) > dim(tmp) [1] 565 1 ...Tao ----- Original Message ---- From: James W. MacDonald <jmacdon@med.umich.edu> To: "Shi, Tao" <shidaxia at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Wednesday, October 1, 2008 5:14:13 AM Subject: Re: [BioC] gene count in a GO term Hi Tao, Shi, Tao wrote: > Hi list, > > Please forgive if this was asked before. > > In R, is there a way to find out how many Human gene products in a GO > term (including all its children) like those reported in AmiGo? I'm > talking about ALL the gene products, not just those on a affy chip. > For example, for GO:0005921 and children and its children, the number > is 6. There are only 6 if you restrict to TAS and IDA. If you allow IEA then there are 27: > library(org.Hs.eg.db) > get("GO:0005921", org.Hs.egGO2ALLEGS) TAS TAS IEA IEA IEA TAS "1823" "2697" "2700" "2701" "2702" "2703" TAS TAS IEA IEA IEA IEA "2705" "2706" "2707" "2709" "4284" "9742" IEA IEA IEA IEA IEA IEA "10052" "10804" "24145" "56666" "57165" "57369" IEA IEA IEA IDA IEA IEA "81025" "84694" "116337" "125111" "127534" "219770" IEA IEA IEA "349149" "375519" "100126572" Best, Jim > > Many thanks! > > ...Tao > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662