The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data

摘要

Schematic for the construction of the CGP map. Given a 3D human genome organization in which the brown and green circles represent two protein-coding genes and respectively, the corresponding genome-wide Hi-C contact map quantifies the contact frequencies between all possible pairs of genomic loci. Using the correspondence between genes and genomic loci, the gene proximity matrix is obtained by extracting the contact frequencies between all pairs of genes. A null model, denoted as , is derived from the 3D genome as well as the gene proximity map, representing the estimated gene proximity hidden in the gene contact frequencies, which is based exclusively on the positions of genes on the 1D DNA strand, i.e., the genomic distance. The CGP map, denoted as , is extracted from the gene proximity map by subtracting the null model . Matrix element captures the corrected spatial proximity between genes and