[BioC] org.Hs.eg.db -- Entrez ID to Gene Symbol conversion

[Seraya Maouche]

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
Faculté de Médecine Pitié-Salpêtrière
91 Boulevard de l'Hôpital
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
**********************************************



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Message: 3
Date: Sun, 22 Feb 2009 08:45:43 -0800 (PST)
From: Tim Smith <tim_smith_666 at 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