Extensive annotations referring to each protein were generated, including basic protein function, genome locus, sequence annotations, EST mapping results, 3D template predictions, transmembrane segments, and domain annotation.
In such cases, the template prediction for the flanking TMHs should be used to guide the loop template selection.
Nearest template prediction (NTP) is a method designed to address these issues, without requiring corresponding training dataset.
The NTP methodology is implemented as Nearest Template Prediction module of GenePattern analysis toolkit and publicly available from www.broadinstitute.org/genepattern.org/genepattern
The nearest template prediction (NTP) method provides a convenient way to make class prediction with assessment of prediction confidence computed in each single patient's gene-expression data using only a list of signature genes and a test dataset.
Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation.
The molecular subclasses, S1 (TGF- β/WNT activation), S2 (MYC/AKT activation, AFP positivity) and S3 (preserved hepatocyte function), were determined by using the nearest template prediction algorithm (Hoshida, 2010) implemented in GenePattern genomic analysis toolkit (www.broadinstitute.org/genepattern).org/genepattern
In order to identify and evaluate a predictive molecular signature, six supervised classification models were implemented: k-Nearest Neighbor (kNN) [ 13], Nearest Template Prediction (NTP) [ 14], Diagonal Linear Discriminant Analysis (DLDA)[ 15], Support Vector Machine (SVM [ 16], Neural Network (NN)[ 13], and Logistic Regression (LR)[ 17].
Survival prediction was performed using the nearest-template prediction (NTP) method.
The nearest-template prediction method was used to derive and test a prognostic signature from this training cohort.
"I would not take the success of Lego as a template for predictions because Lego … didn't just use 'The Lego Movie' to promote Lego".
