biomaRt does not convert entrez gene id to ensembl gene id
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5 months ago
Bane ▴ 10

I am trying to convert my entrez gene_id to ensembl gene_id. Here is my R codes


> library(biomaRt)

> ensembl<- useEnsemblGenomes(biomart = "plants_mart")

> searchDatasets(ensembl,pattern = "Beta")

             dataset                         description
14 bvulgaris_eg_gene Beta vulgaris genes (RefBeet-1.2.2) version 14 RefBeet-1.2.2

> ensembl<- useEnsemblGenomes(biomart = "plants_mart", dataset = "bvulgaris_eg_gene")

> filters= listFilters(ensembl)

> attributes= listAttributes(ensembl)

> View(filters)

> View(attributes)

> genes<- c("LOC104882799","gene-LOC104893862","LOC104890217","LOC104890218","LOC104890219","gene-LOC104890216","gene-LOC104890218","gene-LOC104890219","LOC104890216","104890218","104890219","104890217","104890216") # my NCBI gene_ids normally starts with "gene-" but i editted them differently in order to find the right representation of entrez gene_id

> getBM(attributes = c('entrezgene_id','ensembl_gene_id'), filters = 'entrezgene_id', values = genes, mart = ensembl)

[1] entrezgene_id   ensembl_gene_id 
<0 rows> (or 0-length row.names)

> getBM(attributes = c('entrezgene_accession','ensembl_gene_id'), filters = 'entrezgene_accession', values = genes, mart = ensembl)

[1] entrezgene_accession ensembl_gene_id     
<0 rows> (or 0-length row.names)

What am i doing wrong?

biomaRt ensembl entrez NCBI • 566 views
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those aren't NCBI gene IDs. NCBI gene IDs are just long numbers with no letters. Those look like gene names from NCBI.

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The gtf file that i downloaded from NCBI says they are gene IDs. Now i wonder if i can convert those names to entrez IDs? how can i complete my annotation?

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they may be gene IDs but they're not NCBI gene IDs. What is your overall aim?

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Prior reference for question in this thread : FeatureCounts Output contains gene_id or transcript_id?

Bane : LOC indicates temporary locations (LINK). You should remove the word LOC to get gene ID's. If you search with just numeric part then you will find the gene. Here is one example of that search at NCBI. Not certain if this will work with BioMart.

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Emily_Ensembl when trying to call useEnsemblGenomes function now I get an error :

Error in useEnsemblGenomes(biomart = "plants_mart") : could not find function "useEnsemblGenomes"

I've used it successfully in until some months ago. How can I solve this? thanks

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This has been cross posted as a new question at https://support.bioconductor.org/p/9140102/ I will try to answer it there.

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