Figure 2: Domain-wide alterations in chromatin interaction frequency and chromatin state.
From: Chromatin architecture reorganization during stem cell differentiation
a, Chromatin interaction heat maps in H1 lineages and IMR90 fibroblasts. Also shown are ___domain calls in ES cells and the directionality index (DI) in each lineage. b, Changes in interaction frequency between ES and MS cells. Regions with higher interaction frequency in ES cells are shown in blue, while regions with higher interaction frequency in MS cells are shown in yellow. TADs having a concerted increase or decrease in intra-___domain interaction frequency are labelled yellow or blue, respectively, with the fraction of the ___domain showing increased or decreased interaction frequency listed. Domains that do not show a concerted change are shown in grey. c, Boxplots of Pearson correlations coefficients between interaction frequency changes and chromatin mark changes across TADs for each chromosome (n = 23). Whiskers correspond to the highest and lowest points within 1.5× the interquartile range. d, Classification accuracy of the Random Forest model in predicting whether a bin increases or decreases in interaction frequency (n = 768,793), tested on 10 randomly selected subsets of Hi-C data. Accuracy was also checked using actual data (blue), circularized permutation (green) and a random permutation (yellow) of the data. As expected, randomly permuting the data yields 50% accuracy. Accuracy was also assessed considering the top 30, 40, 50% or all predictions based on vote frequency difference (error bars show the standard deviation of accuracies from the 10 randomly selected data subsets). e, Ranked chromatin features shown according to importance in classification as boxplots of the mean decrease in Gini index from 10 randomly selected data subsets. Whiskers correspond to the highest and lowest points within 1.5× the interquartile range.
