Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
Fig 3
TAD border detection and comparison with the results from Hou et al. [26].
(a) Hi-C normalized interaction matrix at 10 kb resolution for the first 4.5 Mb of chromosome 2L in the Drosophila genome. Interactions matrix and TAD borders were obtained from published data [26]. (b) Hi-C normalized interaction matrix from the same genomic region and resolution as in panel a. The interaction counts are as previously published [26] but the TAD borders are those defined by TADbit. (c) Hi-C normalized interaction matrix from the same genomic region and resolution as in panel a. Interaction data and TAD borders are both generated by TADbit. (d) TAD border alignments between the three differently processed experimental data: borders defined in Hou et al. [26] (Hou-2012, top graph), borders defined by TADbit using the Hou-2012 matrix (mid graph), and borders and matrix determined by TADbit (bottom graph). Dark and light grey arches indicate TADs with higher and lower than expected intra-TAD interactions, respectively. TAD borders are indicated with a black arrow for the Hou-2012 defined borders and by color arrows for the TADbit identified borders. TADbit border robustness (from 1 to 10) is identified by a color gradient from blue to red. (e) Comparison of the agreement between the aligned TAD borders in the three datasets. As a reference, the horizontal grey line indicates a ±20 kb (2 bins) agreement between the biological replica (BR) and the first technical replicate (TR1) as determined by TADbit. The plots in panels a to d were automatically generated by TADbit.