can not find certain genes: Ensembl_Gene_Id To Entrezgene using Biomart

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2.4 years ago

catherine ▴ 250

Hi, this is probably a silly question. I'm using getBM function to convert gene name to Entrezgene ID, but find that not all genes converted successfully. For those that didn't get their Entrezgene ID, I checked on NCBI website and they do have a Entrezgene ID.

Any advice/suggestions are appreciated. Here is my code: (I'm using biomaRt version 2.50.3 and R version 4.1.3)

test<-c("ABI3","CCL3L1","GNG5")

mapping <- getBM(
attributes =  c('entrezgene_id', 'hgnc_symbol'), 
filters = 'hgnc_symbol', values = test, mart = hsmart)

the first gene ABI3 (ID=51225) is good, the last two genes CCL3L1 (ID=6349) and GNG5 (ID=2787) cannot be assigned to their Entrezgene ID.

enter image description here

gene R Biomart ID • 1.3k views

ADD COMMENT • link updated 2.4 years ago by GenoMax 146k • written 2.4 years ago by catherine ▴ 250

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Do you see any warnings?

ADD REPLY • link 2.4 years ago by Ram 44k

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no any warnings

ADD REPLY • link 2.4 years ago by catherine ▴ 250

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Using EntrezDirect: so the ID's exist.

$ esearch -db gene -query "CCL3L1 [gene] and 9606 [taxID]" | esummary | xtract -pattern DocumentSummary -element Id
6349

$ esearch -db gene -query "GNG5 [gene] and 9606 [taxID]" | esummary | xtract -pattern DocumentSummary -element Id
2787

$ esearch -db gene -query "ABI3 [gene] and 9606 [taxID]" | esummary | xtract -pattern DocumentSummary -element Id
51225

ADD REPLY • link 2.4 years ago by GenoMax 146k

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It could be that the ensembl version is outdated. OP, can you show the code that creates the hsmart object please?

ADD REPLY • link 2.4 years ago by Ram 44k

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thank you, but it could be better if using R

ADD REPLY • link 2.4 years ago by catherine ▴ 250

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Use https://cran.r-project.org/web/packages/rentrez/vignettes/rentrez_tutorial.html

ADD REPLY • link 2.4 years ago by GenoMax 146k

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hsmart <- useMart(dataset = "hsapiens_gene_ensembl", biomart = "ensembl")

ADD REPLY • link 2.4 years ago by catherine ▴ 250

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