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Updated: Jun 4, 2026

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

Decoding the causal drivers of spatial cellular topology.

Prannav Shankar¹, Huan Liang¹, Uthsav Chitra^2,3

¹Department of Bioinformatics and Biostatistics, Duke University, Durham, NC 27705, USA.

|June 3, 2026

Summary

This summary is machine-generated.

This study introduces GLACIER, a new method using spatial Granger causality to map cell communication within tissues. It reveals how tissue organization shapes gene regulation and signaling across spatial domains.

Keywords:

Biocomputational method Integrative aspects of cell biology Systems biology Transcriptomics

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Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

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Published on: April 30, 2019

Area of Science:

Cellular Biology
Systems Biology
Bioinformatics

Background:

Understanding spatial cell communication is crucial for tissue organization.
Current methods fail to capture global tissue topology's impact on cellular communication.

Purpose of the Study:

To introduce GLACIER, a novel framework for inferring spatial transcriptional and signaling relationships.
To analyze how tissue architecture directs cellular communication patterns.

Main Methods:

Developed GLACIER, incorporating spatial Granger causality, GASTON's global isodepth coordinates, and Velorama's graph-based causal inference.
Enabled bidirectional inference of regulatory relationships along spatial axes.
Applied to spatial transcriptomics data from the mouse cerebellum.

Main Results:

Identified transcription factor-target interactions and ligand-receptor pairs across spatial domains.
Revealed continuous regulatory gradients within cell types and discontinuous drivers at layer interfaces.
Distinguished forward and backward cellular communication along the isodepth axis.

Conclusions:

GLACIER provides a framework for understanding spatially encoded regulatory programs.
Tissue architecture fundamentally directs cellular communication patterns.
The method captures emergent regulatory relationships shaped by tissue organization.