TargetScan 4.2 information
Changes since version 4.1 (April 2008)
- For TargetScanFly, target mRNAs from chromosome X genes, which were inadvertently omitted from previous releases, are included.
- For TargetScanFly, new predictions were generated using a revised set of 3' UTRs that were based on Flybase 5.4 annotations.
Where a transcript had no annotated 3' UTR, its 3' UTR was defined as the region downstream of the last coding exon,
1500 nt long or 20 nt beyond the nearest AAUAAA, or to the nearest sequence of any adjacent protein-coding or RNA gene, whichever was shorter.
- For TargetScan vertebrate, fly, and worm datasets, since overlapping sites for each miRNA family cannot be occupied at the same time,
a set of only non-overlapping sites is shown in the summary table of miRNA targets.
For vertebrates, the most favorable total context score that considers only non-overlapping sites is shown.
All overlapping sites are still shown on the graphical view.
- For TargetScanFly and TargetScanWorm, predicted targets of a miRNA family are sorted by the number and type of sites,
with genes listed in decreasing total site weight.
Site types are weighted
using the site-type score extrapolated from experiments on vertebrate cells (Grimson et al., 2007),
in which 8mer = 0.31, 7mer-m8 = 0.161 and 7mer-1A = 0.099.
Poorly conserved sites are given the same weight as conserved sites except in the case of ties.
Overlapping sites to the same miRNA were handled as described in change (3).
Changes since version 4.0 (January 2008)
- The major change is an expansion of TargetScanFly to include miRNAs newly identified by Ruby et al., 2007 (Genome Res., 448:83).
- Context scores for mammalian sites that start 15 nt from a stop codon are now considered.
(Version 4.0 only considered scores for mammalian sites greater than 15 nt from the stop codon.)
- The end coordinates of 8mer mammalian sites on UTRs have been corrected by 1 nt.
The previous coordinates had altered the AU-content score, and these scores have now been corrected.
- Scores for 7mer-1A mammalian sites have been adjusted by -0.032.
Previous scores were too high because of a typo that has been corrected in Table S6 of Grimson et al., 2007.
- TargetScanFly and TargetScanWorm now identify predicted pairing between an miRNA and its target gene
as is Grimson et al., 2007 (like mammalian TargetScan).
- MicroRNA family miR-200b/429 has been renamed to miR-200bc/429.
- MicroRNA family miR-124.2/506 has been renamed to miR-124/506 and has been expanded to include hsa-mir-124.
- Rare cases of incorrect mapping of TargetScan sites to the human genome have been fixed.
- Predicted targets are now displayed at the UCSC genome browser (Human, March 2006).
Changes from version 3.1 to version 4.0 (July 2007):
- Additional features have been considered to better predict target specificity, as detailed in Grimson et al., 2007.
Sites within 15 nt of a stop codon are flagged because these are typically not effective.
The context of each of the remaining sites has been evaluated and scored considering the following four features:
- site-type contribution: reflects the type of seed match
- 3' pairing contribution: reflects consequential miRNA-target complementarity outside the seed region
- local AU contribution: reflects transcript AU content 30 nt upstream and downstream of predicted site
- position contribution: reflects distance to nearest end of annotated UTR of target
With all four features, a more negative score is associated with a more favorable site.
The context score is the sum of the above scores, and the context score percentile is the percentile rank
of each site compared to all sites for this miRNA family. Thus a high context score percentile (between 50 and 100)
shows that a specific site is more favorable than most other sites of this miRNA.
In a gene with multiple sites for one miRNA family, a total context score
is calculated as the sum of context scores for the most favorable (most negative) miRNA in this family
(as shown on the miRNA family pages
If the context score for any of these sites is positive (unfavorable), its contribution to the total context score is '0'.
The "representative miRNA" is the miRNA in this family with the most favorable total context score.
- Mammalian miRNA families have been updated to include recent additions to miRBase.
The 3' UTR dataset has been updated to include chicken and is now based on current RefSeq annotation and genome coordinates.
- Degree of conservation, for both miRNA families and predicted targets, has been expanded to include three levels:
- highly conserved = conserved across human (H), mouse (M), rat (R), dog (D), and chicken (C)
- conserved = conserved across human (H), mouse (M), rat (R), and dog (D)
- poorly conserved = conserved across any other combination of species
UTR consensus sequence (shown below each UTR alignment on gene-centric pages [example]) is uppercase at "highly conserved" positions
and lowercase at "conserved" positions.
Changes from version 3.0 to version 3.1