miRNAtap (version 1.6.0)

getTargetsFromSource: Get target list from a single source

Description

This function queries precompiled annotation SQLite database which contains miRNA - target gene associations with their respective scores.

Usage

getTargetsFromSource(mirna, species = "mmu", source = "diana", synonyms = TRUE, both_strands = FALSE)

Arguments

mirna

miRNA in a standard format

species

species in a standard three-letter acronym, default 'mmu'

source

a source target prediction algorithm table to query, default 'diana', other possible values are 'miranda', 'targetscan', and 'pictar'.

synonyms

when searching for -3p miRNA automatically also searches for miRNA with the same name but ending with * (some databases list -3p miRNA this way) and other way around, similarly for -5p miRNA, default TRUE

both_strands

overrides synonyms and searches for targets of both -5p and -3p strands together

Value

data.frame object with entrez IDs of target genes and their scores, if there are no targets found for a given miRNA in a given table then an empty

References

Friedman, R. C., Farh, K. K.-H., Burge, C. B., and Bartel, D. P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome research, 19(1):92-105.

Griffiths-Jones, S., Saini, H. K., van Dongen, S., and Enright, A. J. (2008). miRBase: tools for microRNA genomics. Nucleic acids research, 36(Database issue):D154-8.

Lall, S., Grun, D., Krek, A., Chen, K., Wang, Y.-L., Dewey, C. N., ... Rajewsky, N. (2006). A genome-wide map of conserved microRNA targets in C. elegans. Current biology : CB, 16(5):460-71.

Maragkakis, M., Vergoulis, T., Alexiou, P., Reczko, M., Plomaritou, K., Gousis, M., ... Hatzigeorgiou, A. G. (2011). DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Research, 39(Web Server issue), W145-8.

Examples

targets <- getTargetsFromSource('let-7a', species='hsa', source='targetscan')
head(targets) 
#top of the listof human targets of let-7a from TargetScan only