Question: org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
0
gravatar for Tim Smith
10.3 years ago by
Tim Smith1.1k
Tim Smith1.1k wrote:
Hi, I wanted a table that provides a mapping from Entrez Ids to Gene Symbols for homo sapiens. To do this, I used the following code: ---------------------------------------------------------------------- -------------------------------------------- library(org.Hs.eg.db) x <- org.Hs.egSYMBOL # Get the gene symbol that are mapped to an entrez gene identifiers mapped_genes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_genes]) eids <- '' ENTREZID2GENESYMBOL <- matrix(0,length(xx),2) colnames(ENTREZID2GENESYMBOL) <- c('ENTREZ_IDS','GENE_SYMBOLS') for(k in 1:length(xx)){ if(k==1){ eids <- unlist(xx[k]) goids <- names(xx[k]) } if(k>1){ eids <- c(eids,unlist(xx[k])) goids <- c(goids,names(xx[k])) } dd <- '' for(m in 1:length(unlist(xx[k]))){ if(m==1) dd <- unlist(xx[k])[m] if(m>1) dd <- paste(dd,unlist(xx[k])[m],sep=',') } ENTREZID2GENESYMBOL[k,2] <- dd } ENTREZID2GENESYMBOL[,1] <- rownames(ENTREZID2GENESYMBOL) <- goids idx <- unlist(sort(as.numeric(rownames(ENTREZID2GENESYMBOL)),index=TRUE)[2]) ENTREZID2GENESYMBOL <- ENTREZID2GENESYMBOL[idx,] write.table(ENTREZID2GENESYMBOL,'test.txt',sep='\t') ---------------------------------------------------------------------- ------------------------------------------------ However, when I search the table for the gene 'mTOR' I don't find anything. I believe that mTOR is widely recognized as a cancer causing gene, and I was wondering if I was doing something wrong in my code (or libraries/functions used)... many thanks! Tim PS: My sessionInfo() is : R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.2.6 RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.2 Biobase_2.2.1 > [[alternative HTML version deleted]]
cancer homo sapiens convert • 3.4k views
ADD COMMENTlink modified 10.3 years ago by Seraya Maouche10 • written 10.3 years ago by Tim Smith1.1k
Answer: org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
0
gravatar for Vincent J. Carey, Jr.
10.3 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
briefly, > get("MTOR", org.Hs.egALIAS2EG) [1] "2475" > get("2475", org.Hs.egSYMBOL) [1] "FRAP1" i.e., MTOR is not the symbol used by Entrez. in addition, i would suggest that all refrain from creating lists in R to make such tables. the tables exist in SQLite and you can send SQL queries directly to them. there should be enough information in the AnnotationDbi vignette to indicate how to do this. there is nothing wrong with moving all the data to R, it is just inefficient and defeats the purpose of the external data stores. On Sun, Feb 22, 2009 at 11:45 AM, Tim Smith <tim_smith_666@yahoo.com> wrote: > Hi, > > I wanted a table that provides a mapping from Entrez Ids to Gene Symbols > for homo sapiens. To do this, I used the following code: > > > -------------------------------------------------------------------- ---------------------------------------------- > > library(org.Hs.eg.db) > > x <- org.Hs.egSYMBOL > # Get the gene symbol that are mapped to an entrez gene identifiers > mapped_genes <- mappedkeys(x) > # Convert to a list > xx <- as.list(x[mapped_genes]) > eids <- '' > > ENTREZID2GENESYMBOL <- matrix(0,length(xx),2) > colnames(ENTREZID2GENESYMBOL) <- c('ENTREZ_IDS','GENE_SYMBOLS') > for(k in 1:length(xx)){ > if(k==1){ > eids <- unlist(xx[k]) > goids <- names(xx[k]) > } > if(k>1){ > eids <- c(eids,unlist(xx[k])) > goids <- c(goids,names(xx[k])) > } > dd <- '' > for(m in 1:length(unlist(xx[k]))){ > if(m==1) > dd <- unlist(xx[k])[m] > if(m>1) > dd <- paste(dd,unlist(xx[k])[m],sep=',') > } > ENTREZID2GENESYMBOL[k,2] <- dd > } > ENTREZID2GENESYMBOL[,1] <- rownames(ENTREZID2GENESYMBOL) <- goids > idx <- > unlist(sort(as.numeric(rownames(ENTREZID2GENESYMBOL)),index=TRUE)[2]) > ENTREZID2GENESYMBOL <- ENTREZID2GENESYMBOL[idx,] > > write.table(ENTREZID2GENESYMBOL,'test.txt',sep='\t') > > > -------------------------------------------------------------------- -------------------------------------------------- > > However, when I search the table for the gene 'mTOR' I don't find anything. > I believe that mTOR is widely recognized as a cancer causing gene, and I was > wondering if I was doing something wrong in my code (or libraries/functions > used)... > > many thanks! > > Tim > > > PS: My sessionInfo() is : > > R version 2.8.0 (2008-10-20) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] org.Hs.eg.db_2.2.6 RSQLite_0.7-1 DBI_0.2-4 > AnnotationDbi_1.4.2 Biobase_2.2.1 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 10.3 years ago by Vincent J. Carey, Jr.6.3k
Answer: org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
0
gravatar for Christof Winter
10.3 years ago by
Christof Winter80 wrote:
Hi Tim! Tim Smith wrote, On 22.02.2009 17:45: > Hi, > > I wanted a table that provides a mapping from Entrez Ids to Gene Symbols for > homo sapiens. What about the following? > library(org.Hs.eg.db) > e2s = toTable(org.Hs.egSYMBOL) > head(e2s) gene_id symbol 1 1 A1BG 2 2 A2M 3 3 A2MP 4 9 NAT1 5 10 NAT2 6 11 AACP Cheers, Christof
ADD COMMENTlink written 10.3 years ago by Christof Winter80
Answer: org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
0
gravatar for Seraya Maouche
10.3 years ago by
Seraya Maouche10 wrote:
Dear Tim, I think it's not due to something wrong in your code. As you know, the "official symbol" for Mtor gene is FRAP1 and this gene has several gene alias including FRAP; MTOR; FRAP2; RAFT1; RAPT1; FLJ44809; FRAP1, so I think that in your table, the gene is represented with different symbol. Try to search with Entrez id (2475) Best regards, Seraya ********************************************** Seraya Maouche PhD candidate & computer sciences engineer INSERM U937 Facult? de M?decine Piti?-Salp?tri?re 91 Boulevard de l'H?pital 75634 PARIS cedex 13 Tel: 33 6 65 69 52 67 Fax: 33 1 40 77 97 28 Email: seraya.maouche at chups.jussieu.fr ********************************************** ------------------------------ Message: 3 Date: Sun, 22 Feb 2009 08:45:43 -0800 (PST) From: Tim Smith <tim_smith_666@yahoo.com> Subject: [BioC] org.Hs.eg.db -- Entrez ID to Gene Symbol conversion To: bioc <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <556253.15950.qm at web57503.mail.re1.yahoo.com> Content-Type: text/plain Hi, I wanted a table that provides a mapping from Entrez Ids to Gene Symbols for homo sapiens. To do this, I used the following code: ---------------------------------------------------------------------- ------ -------------------------------------- library(org.Hs.eg.db) x <- org.Hs.egSYMBOL # Get the gene symbol that are mapped to an entrez gene identifiers mapped_genes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_genes]) eids <- '' ENTREZID2GENESYMBOL <- matrix(0,length(xx),2) colnames(ENTREZID2GENESYMBOL) <- c('ENTREZ_IDS','GENE_SYMBOLS') for(k in 1:length(xx)){ if(k==1){ eids <- unlist(xx[k]) goids <- names(xx[k]) } if(k>1){ eids <- c(eids,unlist(xx[k])) goids <- c(goids,names(xx[k])) } dd <- '' for(m in 1:length(unlist(xx[k]))){ if(m==1) dd <- unlist(xx[k])[m] if(m>1) dd <- paste(dd,unlist(xx[k])[m],sep=',') } ENTREZID2GENESYMBOL[k,2] <- dd } ENTREZID2GENESYMBOL[,1] <- rownames(ENTREZID2GENESYMBOL) <- goids idx <- unlist(sort(as.numeric(rownames(ENTREZID2GENESYMBOL)),index=TRUE)[2]) ENTREZID2GENESYMBOL <- ENTREZID2GENESYMBOL[idx,] write.table(ENTREZID2GENESYMBOL,'test.txt',sep='\t') ---------------------------------------------------------------------- ------ ------------------------------------------ However, when I search the table for the gene 'mTOR' I don't find anything. I believe that mTOR is widely recognized as a cancer causing gene, and I was wondering if I was doing something wrong in my code (or libraries/functions used)... many thanks! Tim
ADD COMMENTlink written 10.3 years ago by Seraya Maouche10
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