Related Experiment Video
Updated: Feb 21, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL
Published on: November 3, 2023
Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact
Rajendra Kumar1,2, Haitham Sobhy3, Per Stenberg3,4
1Integrated Science Lab, Umeå University, 901 87, Umeå, Sweden.
Abstract:
Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Karyotyping
Genetic Screens
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
Genomics

