Figure 6.

4DN phase planes reveal a wide range of allelic divergences in gene sub-networks

(A) Workflow to obtain structure and function measures. Eigenvector centrality for each gene is computed from the extracted sub-network of Hi-C contacts. Expression for each gene can be found directly from RNA-seq. Simplified phase planes are shown with linear relationships between changes in structure and function, changes in structure with no changes in function, and changes in function with no changes in structure.

(B) 4DN phase planes of genes specific to B cell function, cell cycle genes, random allele-specific genes, and MAE genes, highlighting the similarities and differences between their alleles. Genes such as BUB1B and PIK3AP1 have similar phase planes between alleles, while RAC1 differs in structure and WRAP73 differs in function. The bottom plot for each column combines the phase planes of the nine example genes, and the average allelic divergence is calculated from each of these gene sets. Circles, squares, and triangles represent phases of the cell cycle: G1, S, and G2/M, respectively. Solid and dashed lines indicate the minimum volume ellipses that contain all cell cycle phases for the maternal and paternal allele of each gene, respectively (Sun and Freund, 2004). Within this figure, G2 includes both G2 and M phase.