SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data

Souvik Seal, Benjamin G Bitler and Debashis Ghosh

PLOS Genetics, 2023, vol. 19, issue 10, 1-25

Abstract: In high-throughput spatial transcriptomics (ST) studies, it is of great interest to identify the genes whose level of expression in a tissue covaries with the spatial location of cells/spots. Such genes, also known as spatially variable genes (SVGs), can be crucial to the biological understanding of both structural and functional characteristics of complex tissues. Existing methods for detecting SVGs either suffer from huge computational demand or significantly lack statistical power. We propose a non-parametric method termed SMASH that achieves a balance between the above two problems. We compare SMASH with other existing methods in varying simulation scenarios demonstrating its superior statistical power and robustness. We apply the method to four ST datasets from different platforms uncovering interesting biological insights.Author summary: In recent years, spatial transcriptomics (ST) has become increasingly popular to study the expression profile of genes across different spatial locations of a tissue. Many of the genes exhibit spatially varying expression patterns making them immensely valuable for understanding the structural and functional properties of the tissue. The proposed method termed SMASH enables powerful and scalable detection of such genes in high-dimensional ST datasets.

Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pgen00:1010983

DOI: 10.1371/journal.pgen.1010983

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