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QuadST: A Powerful and Robust Approach for Identifying Cell-Cell Interaction-Changed Genes on Spatially Resolved
Jinmyung Choi1, Michelle E Ehrlich2, Panos Roussos3
1Institute for Health Care Delivery Science, Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Biorxiv : the Preprint Server for Biology
|December 18, 2023
Summary
QuadST identifies interaction-changed genes (ICGs) in spatial transcriptomics (SRT) data by analyzing gene expression changes relative to cell-cell distance. This novel framework enhances the discovery of genes involved in specific cell type interactions.
Area of Science:
- Genomics
- Computational Biology
- Bioinformatics
Background:
- Spatially resolved transcriptomics (SRT) allows in situ profiling of cellular and transcriptomic organization.
- Existing analytical methods for SRT data have limitations in identifying cell-cell interaction dynamics.
- Understanding cell-type-pair specific interactions is crucial for deciphering tissue function.
Conclusions:
- QuadST is a robust and powerful tool for identifying interaction-changed genes in SRT data.
- The framework effectively reveals genes and regulatory processes underlying specific cell-type pair interactions.
- QuadST advances the analysis of spatial transcriptomics for biological discovery.
