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Lastly, we analyzed multiple large scale datasets of breast cancer as an example of molecular subclass prediction in real-world clinical samples.
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Mutual exclusivity of SPOP mutation with ERG rearrangement as well as a high association with CHD1 deletion reinforces SPOP mutation as defining a distinct molecular subclass of prostate cancer.
In summary, SubMap is a method that provides more general molecular subclass identification and correspondence among a collection of microarray data sets.
This result is concordant with the TCGA study results regarding this molecular subclass.
This phenotype, characterized by aberrant promoter methylation at multiple genes, identifies a distinct molecular subclass of glial tumors.
ROS1 rearrangements also define a unique molecular subclass of lung cancer that may respond to an ALK inhibitor [ 42].
The gene expression patterns that distinguished the subclasses were distilled to a 100-gene expression signature by conducting a leave-one-out cross-validation procedure and selecting the 100 genes having the greatest subclass prediction capability.
As to the prediction of the molecular subclasses of high-grade glioblastoma, 62 DEGs were used for SVM model construction.
Furthermore, we demonstrate that NTP performs reasonably well in predicting molecular subclasses in real-world, large-scale datasets of breast cancer (Example 5).
In the original analysis, the prediction accuracy for the validation set was as high as 87.5% and similar to that achieved in the training procedure, indicating the superior performance of the SVM model in predicting the molecular subclasses of high-grade glioblastoma.
In addition, the accuracy of predicting the molecular subclasses of high-grade glioblastoma was as high as 87.5%.
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