Question: TxDb.Mmusculus.UCSC.mm9.knownGene showing exons with gene_id but there is no such gene
1
gravatar for tonja.r
3.9 years ago by
tonja.r460
UK
tonja.r460 wrote:

I have found some strange thing in this dataset. Namely, I have exons that correspond to one gene_id, but there is no gene with such gene_id in a dataset.

mm9 = TxDb.Mmusculus.UCSC.mm9.knownGene

exon dataset has a gene with ID 100038977

exon = exons(mm9)
gene_id_exons = select(mm9, keys=as.character(exon$exon_id), columns = c("GENEID"), keytype = "EXONID")
> gene_id_exons[which(gene_id_exons$GENEID == "100038977"),][1:4,]
       EXONID    GENEID
243122 241618 100038977
243123 241619 100038977
243124 241620 100038977
243125 241621 100038977

gene dataset does not have a gene with such ID

gene<-genes(mm9)
> which(gene$gene_id == "100038977")
integer(0)

Why are there exons that belong to the 100038977 gene (Gm1993) but there is no such gene listed in the gene dataset?

 

The same happens with gene_ids 100039550 (Gm10486),100039890 (Gm15093),100039939 (Gm2506), 100040048 (Ccl27b), 100040631 etc

 

R • 1.2k views
ADD COMMENTlink written 3.9 years ago by tonja.r460

You might want to post this on the bioconductor support forum. I expect that the various Txdb packages are constructed with a script...perhaps it has a bug.

ADD REPLYlink written 3.9 years ago by Devon Ryan91k
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