Comparison of data-driven vs. uniform size genomic binning procedure. (A) Contact maps were generated using CCD-based binning (left) and uniform size binning (right) for Chromosome 6, respectively. The sizes of tiles in the contact map correspond to their genomic lengths. The same color scale was used for both contact maps. The squares in the contact maps were enlarged as a zoomed-in region, shown below in a genomic browser track view, in which the CCD-based bins are in green and the uniform-sized bins are in blue. The vertical dashed lines indicate the split of functional CCDs into pieces by uniform-sized bins. (B) Distribution of interaction frequency ratio for neighboring bins for all chromosomes by CCD (yellow) and uniform (blue) bins. (C) Histogram of the optimal uniform bin size for 21 long-range interactions identified in the ChIA-PET library. (D) Plots of the SNR as a function of uniform bin area for two of the long-range interactions. The values for the CCD-based bins are indicated by dark squares. The chromosome coordinates of each interaction are listed above the plots.