IL1A-TNIP3 loop in human monocytes can predict perturbation stage in test samples.

(A) Gene pairs tracing loops identified using training data from the human monocyte dataset (GSE47122). Each loop represents the space traced by a gene pair using median gene expression across individuals. (B) Gene expression profile of IL1A and TNIP3 highlighting phase shift. (C) IL1A-TNIP3 loop. Circles represent data points for all individuals and time points in the training data. (D) Polar plot derived from IL1A-TNIP3 loop. Points are colored based on an ordinal time scale to clearly distinguish between points sampled at different times (0 on this ordinal scale corresponds to time point 0 hrs, 1 to 2 hrs, 2 to 2.5 hrs, 3 to 3 hrs, 4 to 3.5 hrs, 5 to 4 hrs, 6 to 14 hrs, 7 to 24 hrs, and 8 to 48 hrs). Distinct time points can be seen to occupy distinct regions on the plot. (E) Angle, derived from polar transformation of the loop, is positively linearly correlated with time on the x-axis (Pearson’s ρ = 0.98) (F) Prediction of perturbation stage for 34 test samples, computed using k-nearest neighbors, shows an accuracy of 94% with a strong linear relationship between predicted and actual time (R2 = 0.99).