Genome Dashboards: Framework and Examples

Abstract

Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics-and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

“…The first databases in genomic science cataloged DNA sequences, along with annotations of the functional loci in those sequences. Subsequently, it becomes clear that there is a need to collect not only information about DNA sequences but also information regarding the histone modifications and transcription factor binding sites that help to regulate genes ( 2–6 ). We term all such additions to the bare DNA sequence as being epigenetic marks.…”