Deciphering the gene-centric spatial dynamics across tissue and time with GeneSPOT
- 1Fudan University
Abstract
Spatial omics technologies provide unprecedented opportunities to investigate how molecular programs are organized within tissues. However, existing analytical frameworks primarily focus on identifying cellular states and characterizing differentially expressed molecular features across these states. The relational spatial organization of molecular features and its dynamics across biological contexts therefore remain largely unexplored. Here, we present GeneSPOT, a gene-centric computational framework for characterizing the spatial relationships among genes and quantifying their reorganization across biological conditions. Although gene-centric in design, GeneSPOT generalizes to other molecular features. Across diverse applications, GeneSPOT resolved tissue structures, integrated paired and unpaired spatial multi-omics data, unveiled the spatial convergence of gene programs during embryonic development, and identified aging-associated spatial reorganization among genes whose expression did not change significantly with age. GeneSPOT thus complements conventional cell-centric analysis, providing a framework for deciphering how spatial relationships among molecular features are reorganized across biological conditions and over time.
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BibTeX
@misc{zou2026deciphering,
title = {{Deciphering the gene-centric spatial dynamics across tissue and time with GeneSPOT}},
author = {Q. Zou and Z. Wang and S. Li and S. Lin and C. Han and Y. Cui and S. Li and L. Wang and D. Zhang and W. Zhang and B. Qian and R. Gao and Z. Yuan},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.24.753111},
url = {https://www.biorxiv.org/content/10.64898/2026.09.24.753111v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Deciphering the gene-centric spatial dynamics across tissue and time with GeneSPOT
AU - Q. Zou
AU - Z. Wang
AU - S. Li
AU - S. Lin
AU - C. Han
AU - Y. Cui
AU - S. Li
AU - L. Wang
AU - D. Zhang
AU - W. Zhang
AU - B. Qian
AU - R. Gao
AU - Z. Yuan
PY - 2026
DA - 2026/09/24
PB - bioRxiv
DO - 10.64898/2026.09.24.753111
UR - https://www.biorxiv.org/content/10.64898/2026.09.24.753111v1
AB - Spatial omics technologies provide unprecedented opportunities to investigate how molecular programs are organized within tissues. However, existing analytical frameworks primarily focus on identifying cellular states and characterizing differentially expressed molecular features across these states. The relational spatial organization of molecular features and its dynamics across biological contexts therefore remain largely unexplored. Here, we present GeneSPOT, a gene-centric computational framework for characterizing the spatial relationships among genes and quantifying their reorganization across biological conditions. Although gene-centric in design, GeneSPOT generalizes to other molecular features. Across diverse applications, GeneSPOT resolved tissue structures, integrated paired and unpaired spatial multi-omics data, unveiled the spatial convergence of gene programs during embryonic development, and identified aging-associated spatial reorganization among genes whose expression did not change significantly with age. GeneSPOT thus complements conventional cell-centric analysis, providing a framework for deciphering how spatial relationships among molecular features are reorganized across biological conditions and over time.
ER -