[BioC] R: error in gene2pathway results

Manca Marco (PATH) m.manca at path.unimaas.nl
Mon Mar 29 18:50:15 CEST 2010

Dear Alberto the answer is below your email.

>Da: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] per conto di Alberto Goldoni [alberto.goldoni1975 at gmail.com]
>Inviato: lunedì 29 marzo 2010 17.53
>A: BioC
>Oggetto: [BioC] error in gene2pathway results
>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
>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
>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.
>Dr. Alberto Goldoni
>Bologna, Italy
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

There is no mistake in the result you are getting. In fact, you are indicating Homo Sapiens (hsa) as the reference organism but you are using a mouse GeneID to indicate the RET gene, and of course this is resulting in no information found.

If you try using 5979 (which is the human RET), this is what you get:

> pred.comp = gene2pathway.signaltrans("5979", organism = "hsa")
Using KEGG information from SOAP service ...
Mapping to signal transduction pathway components via KEGG database ...
---> Information found for  0 genes
1  genes to predict
Retrieving information from InterPro database for organism ' hsa ' via Ensembl ...
Checking attributes ... ok
Checking filters ... ok
done: Information found for  1 out of  1  genes
Model prediction possible for  1  genes ...........done
Preparing output

...and as you can see there are valid results this way.

I hope this will be of some help. All the best,


Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)

Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08,  Maastricht University Medical Center, P. Debeijelaan 25, 6229  HX Maastricht

E-mail: m.manca at path.unimaas.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka


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