Fig. 1

Performance of MIA-Sig on Drosophila S2 cells ChIA-Drop data. a ChIA-Drop experiments are designed to encapsulate each chromatin complex in a droplet, but the encapsulation is a random process and sometimes results in more than one complex in a droplet (multiplets). b MIA-Sig aims to detect multiplets by computing the normalized Shannon entropy H_norm (the “Methods” section). It separates a complex at the largest distance if H_norm is smaller than a threshold, which is 0.7 in this example. This threshold is determined from the normalized Shannon entropy of the expected null model. c Summary statistics of the distance test indicate that the entropy filter resolves around 500,000 doublets and 85,000 triplets, from which 15,055 complexes pass the second distance test. d 2D heatmap comparison of original (bottom triangle) and significant (upper triangle) complexes demonstrates that MIA-Sig removes off-diagonal noise.e Empirical cumulative distribution function for the neighboring distances of original and significant complexes (two-sided Kolmogorov-Smirnov test statistic =0.47, p value <2.2 × 10⁻¹⁶ ). f Comparison of TADs called from significant putative complexes (MIA-Sig) and from enumerating all pairs of fragments (insulation score). MIA-Sig more specifically separates active regions (high H3K27ac and low H3K27me3) rather than assigning them to TADs.