Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
Fig 4
TADbit 3D models and structural properties.
(a) Genomic coordinates, chromatin color proportions, 3D models and structural clustering for the five regions with highest coverage for each color in the Drosophila genome. The ensemble of models for cluster number 1 (the most populated cluster) for each color is represented by its centroid as a solid tube colored by its particle colors. The ensemble around the centroid is simulated by a transparent surface covering a Gaussian smooth surface 150 nm away from the centroid. Figures of 3D models were produced by Chimera [47]. The structural clustering of the 2,000 models produced per region were aligned with TADbit and clustered by structural similarity. Most modeled regions segregate into two large clusters corresponding to mirror images of each other. (b) Comparison of the input interaction Hi-C matrix to a contact map from the 2,000 built models per region, with Spearman correlation coefficient. (c) Structural properties by particle are shown for accessibility (percentage), density (bp per nanometer), interactions (number), and angle (degree). The background of the plot represents the color assigned to each of the particles in the models. TADbit automatically generated all plots.