Tip of the Week: RepTar, a database of miRNA target sites
microRNAs have become a rich source of research as they probably have a huge effect on gene expression and disease. The human genome may encode over 1,000 miRNAs that target over half of our genes. They might be implicated in a lot of common diseases (which not yet have been picked up in GWAS studies?). They are a fascinating area of biology that has only come of it’s on in the last decade. As such, the number of databases to catalog miRNAs is large. Today’s tip is on a new one, RepTar, which is reported in the upcoming NAR database issue. The niche RepTar is attempting to fill is to get predictions of miRNAs more comprehensive by including new research in the algorithm. This new research suggests there are more possible target sites than previously thought. As mentioned in the article,
Recently, the miRNA binding options were expanded further with the identification of ‘centered sites’, functional miRNA target sites that lack both perfect seed pairing and 3′-compensatory pairing and instead exhibit pairing with the target along 11–12 contiguous pairs at the center of the miRNA (4). While some algorithms relaxed the evolutionary conservation criterion (5–11) and/or offer also predictions of 3′-compensatory sites [e.g. (6,12,13)], few databases offer predictions of the whole repertoire of miRNA targeting patterns. Furthermore to date, no database lists genome-wide prediction of cellular targets of viral miRNAs. These miRNAs lack significant evolutionary conservation and their targets are not necessarily expected to be evolutionarily conserved. In addition, the few identified viral miRNA targets have shown both conventional seed binding and 3′-compensatory binding [e.g. (3,14)].
Here we present a database of genome-wide miRNA target predictions for mouse and human genes, based on the predictions of our novel target prediction algorithm, RepTar
I’ll leave the predictive value up to miRNA researchers, but I thought I’d introduce the site.
While I’m at it, allow me to list a few other miRNA sites from labs and institutes as far flung as China, Italy, Israel, Canada and the U.S.. Perhaps someday I’ll do a comparison.
miRBase, which we have a full-length tutorial on.
PicTar, they have an annotation track for UCSC Genome Browser
PuTmiR (in relation to transcription factors)
two lists to catch some others: http://mirnablog.com/microrna-target-prediction-tools/ and http://www.ncrna.org/KnowledgeBase/link-database/mirna_target_database
Elefant, N., Berger, A., Shein, H., Hofree, M., Margalit, H., & Altuvia, Y. (2010). RepTar: a database of predicted cellular targets of host and viral miRNAs Nucleic Acids Research DOI: 10.1093/nar/gkq1233