Question: Targetscan context+ scores, higher or lower
1
gravatar for lishengli19901017
6.3 years ago by
China
lishengli1990101710 wrote:

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!

targetscan mirna target • 6.0k views
ADD COMMENTlink modified 6.3 years ago by iraun3.8k • written 6.3 years ago by lishengli1990101710

Look at this information, available at MAGIA2 tool site - perhaps, you'll find it interesting:

"For each predictor, the stringency of prediction can be tuned by the user.

Different prediction methods uses different strategies to rank predictions: in some cases the more positive the value, the more trustable the prediction, in other cases lower values are better. See the table below to get insights about the range and distribution of scoring values, per species and per predictor. F.i. setting the score lower than -1.4 for microrna_org (H. sapiens) you get no predictions, whereas setting the score to -0.6 you get top 25% trustable predictions."

Picture ilustrating values is available here: https://plus.google.com/u/0/101772480484282089828/posts/Co234KAAQVy?pid=6082680808089494978&oid=101772480484282089828

ADD REPLYlink written 6.3 years ago by orzech_mag230

Thanks, airan. That really helps.

ADD REPLYlink written 6.3 years ago by lishengli1990101710
2
gravatar for iraun
6.3 years ago by
iraun3.8k
Norway
iraun3.8k wrote:

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.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by iraun3.8k

thank u iraun that's really helpful

ADD REPLYlink written 4.0 years ago by 11581059010
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