Fig. 4

Clusters of chromatin conformations under perturbations of epigenetic components and transcription machinery (target region as stated in Fig. 1). A Louvain-Jaccard clustering result of chromatin traces displayed with t-distributed stochastic neighbor embedding (t-SNE). Each dot represents a chromatin trace. Different pseudo-colors represent different chromatin trace clusters. B The same t-SNE plot of chromatin traces as in A but colored by different perturbation conditions. C Mean spatial distance matrices for the six chromatin trace clusters identified in A. The yellow lines represent the ensemble TAD boundary. D Ratio of chromatin trace copy number in each cluster over that in all clusters for each perturbation (and control). N = 2856 for A, B, and D