Challenges for visualizing three‐dimensional data in genomic browsers

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• dc.contributor.author Goodstadt, Mike N.
• dc.contributor.author Marti-Renom, Marc A.
• dc.date.accessioned 2024-01-22T06:47:19Z
• dc.date.available 2024-01-22T06:47:19Z
• dc.date.issued 2017
• dc.description.abstract 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.
• dc.description.sponsorship We thank François Serra, David Castillo, Irene Farabella, Marco Di Stefano, Yannick Spill, François Le Dily, Andrew Yates, Mark McDowall, Jürgen Walther, Sean O'Donoghue, Christian Stolte, Jeffery Heer, Jim Zheng, Philippe Youkharibache, Graham Johnson, Luc Patiny, Diana Roldan, Ian Sillitoe, Alexander Rose, Josep Lluis Gelpi, Adam Hospital, Elaine Meng, Tom Goddard, Daniel Russel, Merry Wang, Ben Webb, Brinda Vallat, Jianlin Chang, Oluwatosin Oluwadare, Victoria Neguembor, Nico Stuurman, and Lucy Natarajan for responding to our queries about their work. We received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013)/ERC Synergy grant agreement 609989 (4DGenome) as well as the European Union's Horizon 2020 research and innovation programme (agreement 676556). We acknowledge Centro de Excelencia Severo SEV-2012-0208 and CERCA Programme/Generalitat de Catalunya to CRG. The content of this manuscript reflects only the author's views and the Union is not liable for any use that may be made of the information contained therein.
• dc.format.mimetype application/pdf
• dc.identifier.citation Goodstadt M, Marti‐Renom MA. Challenges for visualizing three‐dimensional data in genomic browsers. FEBS Letters. 2017 Sep;591(17):2505-19. DOI: 10.1002/1873-3468.12778
• dc.identifier.doi http://dx.doi.org/10.1002/1873-3468.12778
• dc.identifier.issn 0014-5793
• dc.identifier.uri http://hdl.handle.net/10230/58766
• dc.language.iso eng
• dc.publisher Wiley
• dc.relation.ispartof Federation of European Biochemical Societies Letters. 2017 Sep;591(17):2505-19
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/609989
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676556
• dc.rights © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.keyword FAIR principles
• dc.subject.keyword Genome browsers
• dc.subject.keyword Multiscale
• dc.subject.keyword RICH visualization
• dc.subject.keyword Three-dimensional data
• dc.title Challenges for visualizing three‐dimensional data in genomic browsers
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion