Virtual Reality Inspection of Chromatin 3D and 2D Data

Description:

Understanding the packing of long DNA strands into chromatin is one of the ultimate challenges in genomic research. An intrinsic part of this complex problem is studying the chromatin’s spatial structure. Biologists reconstruct 3D models of chromatin from experimental data, yet the exploration and analysis of such 3D structures is limited in existing genomic data visualization tools. To improve this situation, we investigated the current options of immersive methods and designed a prototypical VR visualization tool for 3D chromatin models that leverages virtual reality to deal with the spatial data. We showcase the tool in three primary use cases. First, we provide an overall 3D shape overview of the chromatin to facilitate the identification of regions of interest and the selection for further investigation. Second, we include the option to export the selected regions and elements in the BED format, which can be loaded into common analytical tools. Third, we integrate epigenetic modification data along the sequence that influence gene expression, either as in-world 2D charts or overlaid on the 3D structure itself. We developed our application in collaboration with two domain experts and gathered insights from two informal studies with five other experts.

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Reference:

Elena Molina Lopez, David Kouřil, Tobias Isenberg, Barbora Kozlíková, and Pere-Pau Vázquez (2024) Virtual Reality Inspection of Chromatin 3D and 2D Data. Computers & Graphics, 124, article no. 104059, 11 pages, November 2024.

BibTeX entry:



@ARTICLE{Molina:2024:VRI,
  author      = {Molina Lopez, Elena and David Kou{\v{r}}il and Tobias Isenberg and Barbora Kozl{\'i}kov{\'a} and Pere-Pau V{\'a}zquez},
  title       = {Virtual Reality Inspection of Chromatin {3D} and {2D} Data},
  journal     = {Computers \& Graphics},
  year        = {2024},
  volume      = {124},
  month       = nov,
  pages       = {104059:1--104059:11},
  articleno   = {104059},
  numpages    = {11},
  doi         = {10.1016/j.cag.2024.104059},
  doi_url     = {https://doi.org/10.1016/j.cag.2024.104059},
  oa_gold_url = {https://doi.org/10.1016/j.cag.2024.104059},
  oa_hal_url  = {https://hal.science/hal-04684828},
  osf_url     = {https://osf.io/pxjnq/},
  url         = {https://tobias.isenberg.cc/p/Molina2024VRI},
  pdf         = {https://tobias.isenberg.cc/personal/papers/Molina_2024_VRI.pdf},
}

This work was done at and in collaboration with both the ViRVIG group at the Universitat Politècnica de Catalunya, Spain, and the Visitlab at Masaryk University, Czech Republic, as well as in collaboration with Harvard Medical School, USA.