Figure 5

Prediction performance of methylation status and level. (A) ROC curves of cross-genome validation of methylation status prediction. Colors represent classifier trained using feature combinations specified in the legend. Each ROC curve represents the average false positive rate and true positive rate for prediction on the held-out sets for each of the ten repeated random subsamples. (B) ROC curves for different classifiers. Colors represent prediction for a classifier denoted in the legend. Each ROC curve represents the average false positive rate and true positive rate for prediction on the held-out sets for each of the ten repeated random subsamples. (C) Precision–recall curves for region-specific methylation status prediction. Colors represent prediction on CpG sites within specific genomic regions as denoted in the legend. Each precision–recall curve represents the average precision–recall for prediction on the held-out sets for each of the ten repeated random subsamples. (D) Two-dimensional histogram of predicted methylation levels versus experimental methylation levels. x- and y-axes represent assayed versus predicted β values, respectively. Colors represent the density of each matrix unit, averaged over all predictions for 100 individuals. CGI, CpG island; Gene_pos, genomic position; k-NN, k-nearest neighbors classifier; ROC, receiver operating characteristic; seq_property, sequence properties; SVM, support vector machine; TFBS, transcription factor binding site; HM, histone modification marks; ChromHMM, chromatin states, as defined by ChromHMM software [107].