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Question: Reactome_gene IDs are pathway IDs in biomaRt
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gravatar for b.nota
4 months ago by
b.nota290
Netherlands
b.nota290 wrote:

Hello,

I've been trying to use biomaRt to get reactome IDs (from pathways) of given reactome_gene IDs, however I found out that the reactome_gene IDs ARE the pathway IDs. It is now not possible to get the matching pathways by these gene IDs.

 

For example

library(biomaRt)

ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")

reactomeID <- c("R-HSA-49155", "R-HSA-199420")

getBM(attributes=c('reactome_gene', 'reactome'),
      filters = 'reactome_gene',
      values = reactomeID,
      mart = ensembl)

[1] reactome_gene reactome
<0 rows> (or 0-length row.names)

getBM(attributes=c('reactome_gene', 'entrezgene'),
      filters = 'reactome_gene',
      values = 'R-HSA-49155',
      mart = ensembl)

[1] reactome_gene reactome
<0 rows> (or 0-length row.names)

However, when I use a pathway (reactome) ID instead of reactome_gene ID it does work, but this is not what I am asking to find.

getBM(attributes=c('reactome_gene', 'entrezgene'),
      filters = 'reactome_gene',
      values = 'R-HSA-110331',
      mart = ensembl)

 reactome_gene entrezgene
1  R-HSA-110331       4968
2  R-HSA-110331       4595
3  R-HSA-110331       4350


Is this a bug? Or am I missing something?

 

 

 

 

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by b.nota290
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