Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis - Dataset

DOI10.5281/zenodo.14519865Zenodo14519865MaRDI QIDQ6674971FDOQ6674971

Dataset published at Zenodo repository.

Guo-Cheng Yuan, Shiwei Zheng, Joselyn Cristina Chávez-Fuentes, Wen Wang, Sujung Shin

Publication date: 18 December 2024

Copyright license: Creative Commons Attribution 4.0 International

Description

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.

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