Fig. 8: Predictions for structural variants. | Nature Communications

Fig. 8: Predictions for structural variants.

From: A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants

Fig. 8

a Experimentally measured Hi-C contact map for the 1.1-Mb homozygous inversion for Chr1 from the mouse cell line E11.5 (lower triangle). The position of the segment that is inverted is shown on the track in the top panel. The predicted contact map using DIMES with the perturbation on the WT Hi-C data (see main text and Supplementary Note 3) is shown for comparison (upper triangle). b Top: Perturbation Index (PI) for Chr21 28–30 Mbp. Middle: Chip-seq data for CTCF. Bottom: average value of PI as a function of genomic distance from CTCF Chip-seq peaks. Average PI values up to 150 kbp on either side of CTCF Chip-seq peaks are calculated at 30 kbp resolution. PIbase = 0.2. c An example of the contact map with a single locus deletion (upper triangle) for Chr2 from the IMR90 cell line. The top panel shows a track plot of the perturbation index (PI) computed using Eq. (3). d Plot of principal component dimension 1 (computed from ρ) versus the logarithm of the perturbation index. A, B, and A/B boundaries are marked. Histograms of PC1 and the logarithm of the perturbation index are shown on the top and side, respectively.

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