Dimensionality Reduction for Visualizing Spatially Resolved Profiling Data Using SpaSNE

Authors

• Yuansheng Zhou
• Chen Tang
• Xue Xiao
• Xiaowei Zhan
• Tao Wang
• Guanghua Xiao
• Lin Xu

Language

English

Publication Date

1-6-2025

Journal

Gigascience

DOI

10.1093/gigascience/giaf002

PMID

39960663

PMCID

PMC11831803

PubMedCentral® Posted Date

2-17-2025

PubMedCentral® Full Text Version

Post-print

Abstract

Background: Spatially resolved profiling technologies to quantify transcriptomes, epigenomes, and proteomes have been emerging as groundbreaking methods for comprehensive molecular characterizations. Dimensionality reduction and visualization is an essential step to analyze and interpret spatially resolved profiling data. However, state-of-the-art dimensionality reduction methods for single-cell sequencing data, such as the t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP), were not tailored for spatially resolved profiling data.

Results: Here we developed a spatially resolved t-SNE (SpaSNE) method to integrate both spatial and molecular information. We applied it to a variety of public spatially resolved profiling datasets that were generated from 3 experimental platforms and consisted of cells from different diseases, tissues, and cell types. To compare the performances of SpaSNE, t-SNE, and UMAP, we applied them to 4 spatially resolved profiling datasets obtained from 3 distinct experimental platforms (Visium, STARmap, and MERFISH) on both diseased and normal tissues. Comparisons between SpaSNE and these state-of-the-art approaches reveal that SpaSNE achieves more accurate and meaningful visualization that better elucidates the underlying spatial and molecular data structures.

Conclusions: This work demonstrates the broad application of SpaSNE for reliable and robust interpretation of cell types based on both molecular and spatial information, which can set the foundation for many subsequent analysis steps, such as differential gene expression and trajectory or pseudotime analysis on the spatially resolved profiling data.

Keywords

Humans, Gene Expression Profiling, Single-Cell Analysis, Transcriptome, Algorithms, Computational Biology, Dimensionality Reduction, spatially resolved omics, dimensionality reduction, low-dimensional visualization, molecular data structure, spatial organization of cells

Published Open-Access

yes

Recommended Citation

Zhou, Yuansheng; Tang, Chen; Xiao, Xue; et al., "Dimensionality Reduction for Visualizing Spatially Resolved Profiling Data Using SpaSNE" (2025). Faculty, Staff and Student Publications. 6737.
https://digitalcommons.library.tmc.edu/uthgsbs_docs/6737