gravatar for eggrandio

3 hours ago by

Hi,

I am using biomart to convert gene IDs into entrezid accessions. I am working with arabidopsis genes, and sometimes, the query will not return an entrezid. However, when I look up that gene in the ensembl webpage, I am able to find the correspondence. Maybe I am using the wrong Mart/Dataset?

Here is the code I am using for reference and the results I obtain:

library(biomaRt)
ensembl = useMart("plants_mart",host="plants.ensembl.org")
ensembl = useDataset("athaliana_eg_gene",mart=ensembl)
genes = c("AT2G14610","AT4G23700","AT3G26830","AT3G15950","AT3G54830","AT5G24105")
query = getBM(attributes=c("ensembl_gene_id",
                       "entrezgene_id",
                       "refseq_dna",
                       "entrezgene_accession"),
          filters=("ensembl_gene_id"),
          values=genes,mart=ensembl)

> query
   ensembl_gene_id entrezgene_id     refseq_dna entrezgene_accession
1        AT2G14610        815949    NM_127025.3               815949
2        AT3G15950        820839    NM_112465.4               820839
3        AT3G15950        820839 NM_001035631.2               820839
4        AT3G15950        820839 NM_001338192.1               820839
5        AT3G15950        820839 NM_001338191.1               820839
6        AT3G15950        820839 NM_001338193.1               820839
7        AT3G26830        822298    NM_113595.4               822298
8        AT3G54830            NA                                  NA
9        AT4G23700        828470 NM_001341626.1               828470
10       AT4G23700        828470    NM_118501.5               828470
11       AT5G24105       2745995    NM_203099.2              2745995

In this case, AT3G54830 does not show any entrezgene_id or refseq_dna. However, when I manually search for it at the plant.ensembl.org or NCBI webpages, I can find it:

plants.ensembl.org/Arabidopsis_thaliana/Transcript/Summary?db=core;g=AT3G54830;r=3:20311901-20315887;t=AT3G54830.1

enter image description here

Or when I search for it in the NCBI webpage:

www.ncbi.nlm.nih.gov/gene/824648

enter image description here

Any help would be appreciated!

Thanks!



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