TargetScan
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| Description |
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| Laboratory | David Bartel Lab |
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| Website | http://www.targetscan.org |
In bioinformatics, TargetScan is a web server that predicts biological targets of microRNAs (miRNAs) by searching for the presence of sites that match the seed region of each miRNA.[1] For many species, other types of sites, known as 3'-compensatory sites[1] are also identified. These miRNA target predictions are regularly updated and improved by the laboratory of David Bartel in conjunction with the Whitehead Institute Bioinformatics and Research Computing Group.[citation needed]
TargetScan includes TargetScanHuman,[2][3][4][5][6] TargetScanMouse,[2][3][4][5][6] TargetScanFish,[6][7] TargetScanFly,[8][9] and TargetScanWorm.[10] which provide predictions for mammals, zebrafish, insects, and nematodes centered on the genes of human, mouse, zebrafish, Drosophila melanogaster, and Caenorhabditis elegans, respectively.
Compared to other target-prediction tools[which?] TargetScan provides accurate rankings of the predicted targets for each miRNA.[6] These rankings are based on either the probability of evolutionarily conserved targeting (PCT scores.[4]) or the predicted efficacy of repression (context++ scores).[6]
Another distinguishing feature[compared to?] of TargetScan is its use of extra mRNA annotations. In particular, TargetScanWorm and TargetScanFish are based on C. elegans and zebrafish mRNA models for which 3' untranslated regions (3' UTRs) are defined using polyadenylation sites that are experimentally determined using accurate high-throughput methods.[7][10]
References
- ↑ 1.0 1.1 Bartel DP (2009). "MicroRNAs: target recognition and regulatory functions". Cell 136 (2): 215–33. doi:10.1016/j.cell.2009.01.002. PMID 19167326.
- ↑ 2.0 2.1 "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets". Cell 120 (1): 15–20. 2005. doi:10.1016/j.cell.2004.12.035. PMID 15652477.
- ↑ 3.0 3.1 "MicroRNA targeting specificity in mammals: determinants beyond seed pairing". Mol. Cell 27 (1): 91–105. 2007. doi:10.1016/j.molcel.2007.06.017. PMID 17612493.
- ↑ 4.0 4.1 4.2 "Most mammalian mRNAs are conserved targets of microRNAs". Genome Res. 19 (1): 92–105. 2009. doi:10.1101/gr.082701.108. PMID 18955434.
- ↑ 5.0 5.1 "Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs". Nat. Struct. Mol. Biol. 18 (10): 1139–46. 2011. doi:10.1038/nsmb.2115. PMID 21909094. PMC 3190056. http://dspace.mit.edu/bitstream/1721.1/82943/1/Bartel_Weak%20seed-pairing.pdf.
- ↑ 6.0 6.1 6.2 6.3 6.4 Agarwal, Vikram; Bell, George W.; Nam, Jin-Wu; Bartel, David P. (2015-08-12). "Predicting effective microRNA target sites in mammalian mRNAs". eLife 4: e05005. doi:10.7554/eLife.05005. ISSN 2050-084X. PMID 26267216.
- ↑ 7.0 7.1 "Extensive alternative polyadenylation during zebrafish development". Genome Res. 22 (10): 2054–66. 2012. doi:10.1101/gr.139733.112. PMID 22722342.
- ↑ "Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs". Genome Res. 17 (12): 1850–64. 2007. doi:10.1101/gr.6597907. PMID 17989254.
- ↑ Agarwal, V; Subtelny, AO; Thiru, P; Ulitsky, I; Bartel, DP (4 October 2018). "Predicting microRNA targeting efficacy in Drosophila.". Genome Biology 19 (1): 152. doi:10.1186/s13059-018-1504-3. PMID 30286781.
- ↑ 10.0 10.1 "Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs". Nature 469 (7328): 97–101. 2011. doi:10.1038/nature09616. PMID 21085120. Bibcode: 2011Natur.469...97J.
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