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Genomic interactions reveal the spatial organization of genomes and genomic domains, which is known to play key roles in cell function. Physical proximity can be represented as two‐dimensional heat maps or matrices. From these, three‐dimensional (3D) conformations of chromatin can be computed revealing coherent structures that highlight the importance of nonsequential relationships across genomic features. Mainstream genomic browsers have been classically developed to display compact, stacked tracks based on a linear, sequential, per‐chromosome coordinate system. Genome‐wide comparative analysis demands new approaches to data access and new layouts for analysis. The legibility can be compromised when displaying track‐aligned second dimension matrices, which require greater screen space. Moreover, 3D representations of genomes defy vertical alignment in track‐based genome browsers. Furthermore, investigation at previously unattainable levels of detail is revealing multiscale, multistate, time‐dependent complexity. This article outlines how these challenges are currently handled in mainstream browsers as well as how novel techniques in visualization are being explored to address them. A set of requirements for coherent visualization of novel spatial genomic data is defined and the resulting potential for whole genome visualization is described.

Challenges for visualizing three‐dimensional data in genomic browsers