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

ABSTRACT:

Background

Genome-wide ligation-based assays such as Hi-C provide us with an unprecedented opportunity to investigate the spatial organization of the genome. Results of a typical Hi-C experiment are often summarized in a chromosomal contact map, a matrix whose elements reflect the co-location frequencies of genomic loci. To elucidate the complex structural and functional interactions between those genomic loci, networks offer a natural and powerful framework.

Results

We propose a novel graph-theoretical framework, the Corrected Gene Proximity (CGP) map to study the effect of the 3D spatial organization of genes in transcriptional regulation. The starting point of the CGP map is a weighted network, the gene proximity map, whose weights are based on the contact frequencies bet

SUBMITTER: Ye C 

PROVIDER: S-EPMC7260828 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature