[BioC] error in gene2pathway results

[Alberto Goldoni]

Dear all,
thank you very much and sorry for my errors, i have selected the wrong gene ID.
But i have another question, in the R package there are only 2 model
one for drosophila (”dme”) and for human signaling pathways
(”hsa”). Other models can be created using the functions retrain and
retrain.signaltrans.

Are there anyone with experience that can tell me the right way to
build model for rattus norvegius?

best regards


2010/3/29 Marc Carlson <mcarlson at fhcrc.org>:
> Hi Alberto,
>
> It's not completely clear to me from you message how you got the gene id
> 19713, but if that is supposed to be an entrez gene, I note that it is
> the entrez gene for the mouse version of RET.  But in your code you
> specified 'hsa', which is the 3 letter code from KEGG for humans.
>
>
>  Marc
>
>
>
> On 03/29/2010 08:53 AM, Alberto Goldoni wrote:
>> HI to everybody,
>> i'm using the "gene2pathway" package but i'm not able to obtain something right.
>>
>> i'm using gene2pathway.signaltrans in order to predict a gene's
>> membership to a KEGG signaling pathway and/or pathway component via
>> the contained InterPro domains and in my case for the gene="19713",
>> that represent RET proto oncogene
>> (http://www.uniprot.org/uniprot/P35546).
>> But something is wrong as you can see down there....someone can help me?
>>
>>
>>> pred.comp = gene2pathway.signaltrans("19713", organism = "hsa")
>>>
>> Using KEGG information from SOAP service ...
>> Mapping to signal transduction pathway components via KEGG database ...
>> ---> Information found for  0 genes
>> done.
>> 1  genes to predict
>> Retrieving information from InterPro database for organism ' hsa ' via
>> Ensembl ...
>> Checking attributes ... ok
>> Checking filters ... ok
>> Error in gene2pathway:::getInterProDomains(topredict, gene2Domains =
>> gene2Domains,  :
>>   No mapping Entrez gene ID -> InterPro found!
>>
>>
>> Best regards.
>>
>>
>>
>
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-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Bologna, Italy