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(d) Comparison of variants annotated as pathogenic in dbNSFP and after correction for the three variant effect predictors: PROVEAN, PolyPhen-2 (HumVar), and SIFT.
The best model from each region included 3 main effect predictors; 5 out of the 7 possible main effect variables were selected by at east one of the three regional optimizations.
To validate this hypothesis we have annotated all RMAs with the custom pathogenicity predictions by three commonly used variant effect predictors: PROVEAN,10, 11 SIFT,13, 13 and PolyPhen-214 (see Supplementary Methods for more information).
Final modeling was performed through the integration of previous models, the drug-target and the target-adverse effect predictors.
Model 1 includes only main effect predictors; model 2 adds the interaction term between percentage of female authors and percentage of international authors.
It's important we design studies that help to clarify the mechanisms to effect predictors and outcomes.
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McLaren, W. et al. The Ensembl variant effect predictor.
McLaren, W. et al. The Ensembl Variant Effect Predictor.
These variants were analyzed by Ensembl variant effect predictor (http://www.ensembl.org/Tools/VEP) for their coding consequence.
These variants were passed onto Ensembl variant effect predictor (http://www.ensembl.org/Tools/VEP) for evaluation of their allelic substitution effects on the corresponding proteins.
The functional consequences of polymorphisms were assessed by using Variant Effect Predictor (VEP).
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