Matching 3'Utr Mutations To Mirna Target Sites

Question

[david]

Hi,

I have been provided with a file of 3'UTRs that are mutated from the core facility. I'm trying to match that location to a miRNA target (or predicted target. Mor information below.

Type of data:

Patient specific 3'UTR that have mutations in them. This includes chromosomal information, SNP ref numbers, and gene name.

Q. How can you determine if the SNP/mutation appears in a miRNA target and/or seed sequence of a target. There doesn't seem to be reliable information on miRNA target locations let alone seed sequence information ? I guess targetscan could be used for predicted as well?

Which databases or workflows would you use for this?

Thanks in advance.

Answer 1

[Bharat Iyengar]

TargetScan and miRanda have a list of predicted targets. But you may need to verify if both of them agree with each other, if you are taking a consensus. miRecords has a list of experimentally validated targets. Although some are not direct targets, the site information for direct targets is given if they have been validated.

Answer 2

[Asaf]

The UCSC genome browser has a track of conserved TargetScan miRNA predicted binding sites (called TS miRNA sites). You can download it to Galaxy and then intersect this with your data pretty easily or with SNP track if you'd like.
And yes, a comprehensive database that will list known miRNAs binding sites is absent. You can, however, use the data from this high-throughput CLASH experiment, it should have good data on miRNA binding sites.
Good luck!