Virtual reality inspection of chromatin 3D and 2D data

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F24%3A00138310" target="_blank" >RIV/00216224:14330/24:00138310 - isvavai.cz</a>

Result on the web

<a href="https://www.sciencedirect.com/science/article/pii/S0097849324001948" target="_blank" >https://www.sciencedirect.com/science/article/pii/S0097849324001948</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.cag.2024.104059" target="_blank" >10.1016/j.cag.2024.104059</a>

Result language

angličtina

Original language name

Virtual reality inspection of chromatin 3D and 2D data

Original language 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.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10200 - Computer and information sciences

Project

—

Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2024

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Computers &amp; Graphics

ISSN

0097-8493

e-ISSN

1873-7684

Volume of the periodical

124

Issue of the periodical within the volume

104059

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

1-11

UT code for WoS article

001307796600001

EID of the result in the Scopus database

2-s2.0-85202940443