Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis.
bioRxiv
; 2024 Apr 28.
Article
en En
| MEDLINE
| ID: mdl-38712255
ABSTRACT
Recent technological developments have made it possible to map the spatial organization of a tissue at the single-cell resolution. However, computational methods for analyzing spatially continuous variations in tissue microenvironment are still lacking. Here we present ONTraC as a strategy that constructs niche trajectories using a graph neural network-based modeling framework. Our benchmark analysis shows that ONTraC performs more favorably than existing methods for reconstructing spatial trajectories. Applications of ONTraC to public spatial transcriptomics datasets successfully recapitulated the underlying anatomical structure, and further enabled detection of tissue microenvironment-dependent changes in gene regulatory networks and cell-cell interaction activities during embryonic development. Taken together, ONTraC provides a useful and generally applicable tool for the systematic characterization of the structural and functional organization of tissue microenvironments.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Idioma:
En
Revista:
BioRxiv
Año:
2024
Tipo del documento:
Article
País de afiliación:
Estados Unidos