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","r efseq_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! [[alternative HTML version deleted]]

On Wed, Jul 29, 2009 at 12:01 AM, <mauede@alice.it> wrote: > I downloaded the following file from miRDB > http://mirdb.org/miRDB/download/MirTarget2_v3.0_prediction_result.tx t.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_i d"), > 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 ? > Hi, Maura. Yes, unfortunately, there is not a 1-1 correspondence. Ensembl and NCBI (the curator of RefSeq) are independent organizations, each with different build policies and annotation processes for transcripts. So, in general in this field (genomics/bioinformatics), there is RARELY a 1-1 correspondence between any two entities. I would suggest that 246/253 is actually quite a good result--I might have expected a bit less a priori. Sean [[alternative HTML version deleted]]