TargetScan 4.1 information


Changes since version 4.0 (January 2008)

  1. The major change is an expansion of TargetScanFly to include miRNAs newly identified by Ruby et al., 2007 (Genome Res., 448:83).
  2. 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.)
  3. 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.
  4. 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.
  5. TargetScanFly and TargetScanWorm now identify predicted pairing between an miRNA and its target gene as in Grimson et al., 2007 (like mammalian TargetScan).
  6. MicroRNA family miR-200b/429 has been renamed to miR-200bc/429.
  7. MicroRNA family miR-124.2/506 has been renamed to miR-124/506 and has been expanded to include hsa-mir-124.
  8. Rare cases of incorrect mapping of TargetScan sites to the human genome have been fixed.
  9. Predicted targets are now displayed at the UCSC genome browser (Human, March 2006).

Changes from version 3.1 to version 4.0 (July 2007):

  1. 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:
    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 [example]). 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.

  2. 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.

  3. Degree of conservation, for both miRNA families and predicted targets, has been expanded to include three levels:

    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