targetscan.Mm.egTARGETSFULL {targetscan.Mm.eg.db}R Documentation

Annotation data for TargetScane miRNA target predictions

Description

targetscan.Mm.egTARGETSFULL maps Entrez gene idenifiers to miRNA families. The mappings are taken from the TargetScan database.

Details

TargetScan predicts biological targets of miRNAs by searching for a presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.

There are currently two annotation packages for TargetScan, one for human and another one for mouse. These correspond to the TargetScanHuman and the TargetScanMouse databases, see the TargetScan website for details.

targetscan.Mm.egTARGETSFULL is an R object containing key and value pairs. Keys are Entrez gene identifiers and values are lists, each list member corresponds to a predicted targeting miRNA family. Each list member is itself a list with the following members:

miR.Family
Name of the miRNA family.
UTR.start
Start position on UTR.
UTR.end
End position on UTR.
MSA.start
Start of multiple sequence alignment, with gaps.
MSA.end
End of multiple sequence alignment.
Seed.match
Type of the matching. Possible values are ‘8mer’, which means that all eight bases match, ‘m8’, which means an exact match to positions 2-8 of the mature miRNA, and ‘1A’, which means that positions 2-7 of the mature miRnA match, followed by an 'A'.
PCT
The probability of conserved targeting, see Friedman et al. in the references section below for details.

References

Friedman RC, Farh KK, Burge CB, Bartel DP.: Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan;19(1):92-105

http://www.targetscan.org for TargetScan and http://microrna.sanger.ac.uk/sequences/ for miRBase.

See Also

targetscan.Mm.egTARGETSFULL for more information about the miRNA targets.

Examples

## Get the miRNA families that regulate these genes
genes <- sample(ls(targetscan.Mm.egTARGETSFULL), 3)
mget(genes, targetscan.Mm.egTARGETSFULL)

[Package targetscan.Mm.eg.db version 5.0-1 Index]