Virtual reality inspection of chromatin 3D and 2D data

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Virtual reality inspection of chromatin 3D and 2D data

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Virtual reality inspection of chromatin 3D and 2D data

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10200 - Computer and information sciences

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2024

Kód důvěrnosti údajů

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

Název periodika

Computers &amp; Graphics

ISSN

0097-8493

e-ISSN

1873-7684

Svazek periodika

124

Číslo periodika v rámci svazku

104059

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

11

Strana od-do

1-11

Kód UT WoS článku

001307796600001

EID výsledku v databázi Scopus

2-s2.0-85202940443