How to get all microRNA target genes?

Question

[Katarina]

Hello,

I would like to have a complete list of genes that are validated targets of microRNA regulation in R. I have tried getting a complete list of microRNA using the biomaRt package (list of ~1800 microRNA) then input the list to the get_multimir function from the multimir package to retrieve validated miRNA -target gene interaction. In the end I got ~11 000 target genes! This would suggest that over 50% of genes are under microRNA regulation. I guess I did something wrong at some step but I can't figure it out! Is there a better way to retrieve the complete target gene list?

PS. This is my first post on this forum, sorry if I didn't pose my question correctly! Any advice is appreciated.

Answer 1

[i.sudbery]

For the purposes of multimir "validated" can include any interaction supported by CLASH/PAR-CLIP/AGO-CLIP data. In this case I'm surprised the number is as low as 50%.