Predicting position along a looping immune response trajectory
Fig 5
Identifying CDC20-IFI44L loop and predicting perturbation stage in YF17D-vaccinated individuals.
(A) Timeline of gene expression shows that CDC20 peaks at day 3 whereas IFI44L peaks at day 7 for training data in the Montreal cohort (n = 11) (GSE13699). (B) CDC20-IFI44L loop. Circles represent data points for all individuals and time points in the point cloud. Two data points have been removed for better visualization; all data points are shown in S6 Fig. (C) Angle derived from polar transformation of the CDC20-IFI44L loop is positively linearly correlated with and time (Pearson’s ρ = 0.91) (D) Confusion matrix, in the form of a heatmap, showing prediction accuracy for stage of infection in the withheld samples in the Montreal cohort (n = 7) (GSE13699). A stage prediction accuracy of 83% was achieved. (E) Confusion matrix, in the form of a heatmap, showing prediction accuracy for stage of infection in the Lausanne cohort (n = 11) (GSE13699). A stage prediction accuracy of 73% was achieved. (F) Confusion matrix, in the form of a heatmap, showing prediction accuracy for stage of infection in the Emory cohort (n = 25) (GSE13485); a prediction accuracy of 65% was achieved.