I'm using Targetscan6.2 to predict miRNA targets. The results coming out really confused me, how to choose among tens of targets of the same miRNA? Targets with higher or lower context+ scores are better? Thank you!
Targets with lowest context+ scores are the most representative ones.
For each predicted target of each miRNA, the sum of the context+ scores for the sites to that miRNA was calculated as the total context+ score. Predicted targets of each miRNA family are sorted by total context+ score. The representative miRNA is the miRNA in its family with the most favorable (lowest) total context+ score.
The context+ score for a specific site is the sum of the contribution of these six features (according to Garcia et al., 2011 paper):
- site-type contribution
- 3' pairing contribution
- local AU contribution
- position contribution
- TA (target site abundance) contribution*
- SPS (seed-pairing stability) contribution*
Here you can find more information: http://www.targetscan.org/vert_61/docs/help.html
Hope it helps.