TargetScan

TargetScan
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LaboratoryDavid Bartel Lab
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Websitehttp://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. ^ a b Bartel DP (2009). "MicroRNAs: target recognition and regulatory functions". Cell. 136 (2): 215–33. doi:10.1016/j.cell.2009.01.002. PMC 3794896. PMID 19167326.
  2. ^ a b Lewis BP, Burge CB, Bartel DP (2005). "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets". Cell. 120 (1): 15–20. doi:10.1016/j.cell.2004.12.035. PMID 15652477.
  3. ^ a b Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP (2007). "MicroRNA targeting specificity in mammals: determinants beyond seed pairing". Mol. Cell. 27 (1): 91–105. doi:10.1016/j.molcel.2007.06.017. PMC 3800283. PMID 17612493.
  4. ^ a b c Friedman RC, Farh KK, Burge CB, Bartel DP (2009). "Most mammalian mRNAs are conserved targets of microRNAs". Genome Res. 19 (1): 92–105. doi:10.1101/gr.082701.108. PMC 2612969. PMID 18955434.
  5. ^ a b Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP (2011). "Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs" (PDF). Nat. Struct. Mol. Biol. 18 (10): 1139–46. doi:10.1038/nsmb.2115. PMC 3190056. PMID 21909094.
  6. ^ a b c d e 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. PMC 4532895. PMID 26267216.
  7. ^ a b Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP (2012). "Extensive alternative polyadenylation during zebrafish development". Genome Res. 22 (10): 2054–66. doi:10.1101/gr.139733.112. PMC 3460199. PMID 22722342.
  8. ^ Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC (2007). "Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs". Genome Res. 17 (12): 1850–64. doi:10.1101/gr.6597907. PMC 2099593. PMID 17989254.
  9. ^ 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. PMC 6172730. PMID 30286781.
  10. ^ a b Jan CH, Friedman RC, Ruby JG, Bartel DP (2011). "Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs". Nature. 469 (7328): 97–101. Bibcode:2011Natur.469...97J. doi:10.1038/nature09616. PMC 3057491. PMID 21085120.

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