Figure 1. The effective gene density obtained from extrinsic suprachromosomal entities of the human genome.

A histogram of effective gene density from all unique chromosome pairs is represented in (a). The histogram colour key is encoded at the top of panel (a) as s₆/s₅ (dark/light red), s₄/s₃ (dark/light orange), s₂/s₁ (dark/light yellow) and s₀ (off-white) as effective gene density values increase along the x-axis. A hierarchically clustered heatmap of the effective gene density matrix from all chromosome pairs indexed by labels j and k on the y- and x-axes respectively is shown in (b). The values of effective gene density from and are identical, indicated by a dashed diagonal line, and the horizontal and vertical dashed lines segregate suprachromosomal pairs when both C_j and C_k belong to Group A, or Group B, or their admixture. Here, chromosome Y (denoted chrY, from Group B) is highlighted by two vertical dashed lines, which represent its unique position in the overall hierarchy that is dominated by chromosome 19 (marked “*”). The colour key for effective gene density values in (a, b) are consistent. The five acrocentric CTs: chromosomes 13–15, 21 and 22 are represented with bold labels. Exploiting the degeneracy of chrY, with respect to all other chromosomes of the human genome, a mathematically equivalent heatmap is generated in panel (c). Suprachromosomal entities coloured s₀ to s₆ gradient in (a) are mapped as boxes in (c). For example, s₁ is represented by chr19 paired with chr2/chr1/chr11/chr17, s₂ represented by chr19 when paired with chr9/chr8/chr4/chr20 and so on. Similarly, deeper hues from orange to red represent a progressively larger pools of degenerate suprachromosomal pairs with similar effective gene density. Hypothetically, cohorts of suprachromosomal entities s₀–s₆ may be used to recreate a 3D spherical representation of CT arrangement for cell type-specific human nuclei in a 2D rendition (panels d, e), arranged with relatively high effective gene density contributors such as s₀/s₁/s₂ toward the interior of the nuclei and the relatively low effective gene density contributors such as s₆/s₅ toward the periphery as indicated by the arrow.