Updated database for miRNA

Question

[Tanvir Ahamed]

Does anyone can suggest an updated database for miRNA ? I tried some, but found them old and not recently updated .

Answer 1

[robm9119]

http://www.mirbase.org/ftp.shtml

[Tanvir Ahamed]

its very old. About 2 years. Last update 06/14 (Version 21 and Total miRNA 28645).

[robm9119]

GENCODE project annotates many more novel miRNAs:

http://www.gencodegenes.org/

[Tanvir Ahamed]

did not find any download option for miRNA. can u give any link specifically for miRNA ?

[Denise CS]

You can get the annotation of miRNA from the Ensembl FTP. The annotation from Ensembl is a merged with the annotation from HAVANA, and this is the GENCODE set. Check our human gene annotation page for more details.

[Denise CS]

I forgot to mention that if you use the GTF file from the Ensembl FTP, you need to retrieve the 'miRNA' from the remaining annotation of protein coding genes and otherwise). Simply focus on the biotype 'miRNA'. Check the Ensembl Annotation of ncRNAs page for more details on those biotypes.

[Tanvir Ahamed]

I have used to following code to read the GTF file in R

library(refGenome)
pp<-ensemblGenome("C:\\Users\\Downloads")
read.gtf(pp, "Homo_sapiens.GRCh38.84.chr.gtf")
mm<-getGtf(pp)
# Frequency table for  biotype 'miRNA'
table(mm$transcript_biotype)

But i got number of miRNA is 8172 !!

but in mirBase, the number of miRNA is 28645.

can you please tell , where i am doing the mistake !?