HiCognition: a visual exploration and hypothesis testing tool for 3D genomics

The 3D organization of the genome and epigenetic marks play important roles in gene expression, DNA repair, and chromosome segregation. Understanding how structure and composition of the chromatin fiber contribute to function requires integrated analysis of multiple genomics datasets from various techniques, experimental conditions, and cell states. Genome browsers facilitate such analysis, yet currently visualize only a few regions at a time and lack statistical functions that are often necessary to extract meaningful information. Here, we present HiCognition, a visual exploration and machine-learning tool based on a new genomic region set concept, which enables detection of patterns and associations between 3D chromosome conformation and collections of 1D genomics profiles of any type. By revealing how transcriptional activity and cohesin subunit isoforms contribute to chromosome conformation, we showcase how the flexible user interface and machine learning tools of HiCognition can help understand the relationship between structure and function of the genome.