|Search for predicted microRNA targets in mammals||[Go to TargetScanHuman]|
|[Go to TargetScanWorm]|
|[Go to TargetScanFly]|
|[Go to TargetScanFish]|
* broadly conserved = conserved across most vertebrates, usually to zebrafish
conserved = conserved across most mammals, but usually not beyond placental mammals
TargetScan predicts biological targets of miRNAs by searching for the presence of conserved, , and sites that match the of each miRNA (Lewis et al., 2005). As options, predictions with only poorly conserved sites and predictions with nonconserved miRNAs are also provided. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing (Friedman et al., 2009). In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network (McGeary, Lin, et al., 2019). As an option, predictions are also ranked on the basis of targeting efficacy estimated using cumulative weighted context++ scores of the sites (Agarwal et al., 2015). As another option, predictions are ranked by their probability of conserved targeting (PCT, Friedman et al., 2009). TargetScanMouse considers matches to mouse 3' UTRs and their orthologs, as defined by UCSC whole-genome alignments. Conserved targeting has also been detected within open reading frames (ORFs). A listing of these ORF sites can be found at the bottom of Supplemental Table 2 of Lewis et al., 2005.
This search page of TargetScan Release 8.0 retrieves predicted regulatory targets of mammalian microRNAs. The predicted targets are essentially the same as those presented in previous versions of the TargetScan site (Releases 2.0, 2.1, 3.0, 3.1, 4.0 - 4.2, 5.0 - 5.2, 6.0 - 6.2, 7.0, 7.1, and 7.2. (Lewis et al., 2005; Grimson et al., 2007; Friedman et al., 2009; García et al., 2011; Agarwal et al., 2015). Thus Release 8 uses the same 3' UTR profiles as Release 7 and the same miRNA families, which were curated from Chiang et al., 2010 and Fromm et al., 2015. Compared to previous releases, Release 8 provides a new option for ranking mammalian predictions; by default, these predictions are ranked using the new biochemical model (McGeary, Lin, et al., 2019).
An introduction to microRNAs (iBiology talk)
Frequently Asked Questions (FAQs)
More information about Release 8.0
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