I downloaded the following file from miRDB
http://mirdb.org/miRDB/download/MirTarget2_v3.0_prediction_result.txt.gz

I have checked that miRDB Gene_Bank_Accession_Number (for Human it is something like NM_xxxxx) correspond to BioMart "refseq_dna".

I have a vector containing 253  Gene_Bank_Accession_Numbers
 length(tmp_miRNA_GB)
[1] 253
> tmp_miRNA_GB[1:5]
[1] "NM_203390"    "NM_024639"    "NM_001017989" "NM_203331"    "NM_001879"  

I use such a vectos as input filter to getBM to obtain the respective ensembl_transcript_id.
Surprisingly onlly 246 ensembl_transcript_ids are found:
 
> gene.map <- getBM (attributes = c("hgnc_symbol","ensembl_gene_id","refseq_dna","ensembl_transcript_id"),
                                       filters = "refseq_dna", values = tmp_miRNA_GB, mart=hmart)

> dim(gene.map)
[1] 246   4

I thought there would be a 1-1 correspondence between the two attributes: "refseq_dna" and "ensembl_transcript_id"
Am I mistaken ?

Thank you in advance for correcting my misunderstandings,
Maura



tutti i telefonini TIM!


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