[BioC] org.Sc.sgd.db: ensembl id or entrez ID to GO term mapping

[Marc Carlson]

Hi Julie,

The thing to understand about the yeast package org.Sc.sgd.db, is that
it is not Entrez Gene based.  It is SGD based instead (which is why it
has the strange looking name and also why the primary keys are not
entrez gene IDs).  It does have entrez gene ID mappings however which
can be accessed using org.Sc.sgdENTREZID  as well as GO mappings which
can be accessed using org.Sc.sgdGO and it seems that you found the
mapping for ensembl gene IDs. 

It's not completely clear to me from your posts what you were trying
for.  But here are some examples of using the ID you gave to get results
back for GO, Entrez Gene ID and Ensembl:

ID = "YHR055C"

# get Entrez Gene ID
get(ID, org.Sc.sgdENTREZID)

# get ensembl Gene ID
get(ID, org.Sc.sgdENSEMBL)

# get GO terms
get(ID, org.Sc.sgdGO)

Hope this helps?  Let me know if it doesn't and we can make it work.


  Marc



On 03/23/2010 07:38 AM, Zhu, Julie wrote:
> Hi,
>
> I have used org.Hs.egGO for mapping entrez ID in human to GO term successfully. However the mapping is not available in org.Sc.sgGO. So I tried to convert gene name to orf using org.Sc.sgdCOMMON2ORF mapping. Then I encountered the following error.
>
> gene2orf = org.Sc.sgdCOMMON2ORF
> mapped_gene <- mappedkeys(gene2orf)
> xx <- as.list(gene2orf[mapped_genes])
> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>   value for "15S_rRNA" not found
> Error in as.list(gene2orf[mapped_genes]) :
>   error in evaluating the argument 'x' in selecting a method for function 'as.list
>
> The session information is the same as the following post.
>
> Thank you so much for your help!
>
> Best regards,
>
> Julie
>
>
> On 3/23/10 9:43 AM, "Zhu, Julie" <Julie.Zhu at umassmed.edu> wrote:
>
> Hi,
>
> I have used org.Hs.egENSEMBL2EG in org.Hs.eg.db for mapping emsembl gene ID
> to entrez ID successfully. However it does not work for org.Sc.sgd.db. I
> tried to use org.Sc.sgdENSEMBL instead but got the ensembl ID back as
> mapping. Here is the code snippet to show the problem and session info.
>
> orgAnn <- get(paste("org.Sc.sgd", "ENSEMBL", sep = ""))
> OrgAnn
>
> IDs = c("YHR055C")
> xx[names(xx)==IDs[1]]
>
> ###### output the ensembl id instead of entrez id #######
> $YHR055C
> [1] "YHR053C" "YHR055C"
>
> # sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-apple-darwin8.11.1
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] org.Sc.sgd.db_2.3.5                 ChIPpeakAnno_1.3.15
> limma_2.19.2
>  [4] org.Hs.eg.db_2.3.6                  GO.db_2.3.5
> RSQLite_0.7-1
>  [7] DBI_0.2-4                           AnnotationDbi_1.8.1
> BSgenome.Ecoli.NCBI.20080805_1.3.16
> [10] BSgenome_1.14.2                     Biostrings_2.14.8
> IRanges_1.4.9
> [13] multtest_2.1.2                      Biobase_2.5.5
> biomaRt_2.1.0
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-3      RCurl_0.98-1    splines_2.10.0  survival_2.35-7
> tools_2.10.0    XML_2.3-0      ENSEMBL map for Yeast (object of class
> "AnnDbBimap")
>
>
>
> Thank you very much for your help!
>
> Best regards,
>
> Julie
>
>
> *******************************************
> Lihua Julie Zhu, Ph.D
> Research Associate Professor
> Program in Gene Function and Expression
> University of Massachusetts Medical School
> 364 Plantation Street, Room 613
> Worcester, MA 01605
> 508-856-5256
> http://www.umassmed.edu/pgfe/faculty/zhu.cfm
>
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