How To Get Experimentally Verified Pre-Mirnas In Mirbase Database

Question

[shenwei356]

The reference of miRBase mentioned that hairpin precursors are very rarely experimentally validated.
Another articles said "Only the half (6166 out of 11488) of miRBase (version 14.0) pre-miRNA/miRNA pairs have been experimentally validated".

When I checked the database files downloaded from miRBase (version 18), only 296 (out of 1527) human premiRNAs have comments in the table "mirna". And less than 120 records have clearly been declared validated or verified in human.

Did I have the right way? Someone have good idea?

[JC]

reference to the paper claiming 50% validation?

[shenwei356]

Yes, the article is here. http://bioinformatics.oxfordjournals.org/content/26/18/2226.full Or just google it with the sentence.

[JC]

thanks, I'm gonna read it.

Answer 1

[JC]

Well, looks that the paper is incorrectly saying "experimentally validated", I think they mean "experimentally identified". Checking the numbers in the miRNA.dat file from miRBase I think they just counted the times that a miRNA is flagged as "evidence=experimental".

[shenwei356]

I wrote a letter to Dr. Sam Griffiths-Jones, one of the founders of miRBase for this case. He said:

All the evidence in miRBase points at mature sequences, not precursors. You therefore can't get experimentally validated precursors out of miRBase (or from anywhere else I know). The precursor sequences are essentially only indirectly validated by study of the mature sequences. For example, if reads from a miRNA sequencing experiment map to only one location in the genome, and both potential 5' and 3' mature sequences are supported, then the precursor sequence is implicitly validated.

[JC]

thanks for the clarification.