In
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...
, 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.
For many species, other types of sites, known as 3'-compensatory sites
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.
TargetScan includes TargetScanHuman,
TargetScanMouse,
TargetScanFish,
TargetScanFly,
and TargetScanWorm.
which provide predictions for mammals, zebrafish, insects, and nematodes centered on the genes of human, mouse,
zebrafish, ''
Drosophila melanogaster
''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the " vinegar fly" or " pomace fly". Starting with ...
'', and ''
Caenorhabditis elegans
''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (r ...
'', respectively.
Compared to other target-prediction tools TargetScan provides accurate rankings of the predicted targets for each miRNA.
These rankings are based on either the probability of evolutionarily conserved targeting (P
CT scores.
) or the predicted efficacy of repression (context++ scores).
Another distinguishing feature of TargetScan is its use of extra mRNA annotations. In particular, TargetScanWorm and TargetScanFish are based on ''
C. elegans
''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' ( ...
'' and
zebrafish mRNA models for which
3' untranslated regions
In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. The 3′-UTR often contains regulatory regions that post-transcriptional ...
(3' UTRs) are defined using
polyadenylation
Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eu ...
sites that are experimentally determined using accurate high-throughput methods.
References
{{reflist, 35em
External links
TargetScanmiRBaseBartel Lab
MicroRNA
Servers (computing)
Biological databases