Identifying cell-type-specific spatially variable genes with ctSVG.
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2025-12
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UNLABELLED: Spatially variable genes (SVGs) reveal the molecular and functional heterogeneity of cells across different spatial regions of a tissue. Sample-wide SVGs identified by existing methods largely overlap with cell-type marker genes derived from single-cell gene expression, leaving the spatial location information largely underutilized. We develop ctSVG, a computational method specifically tailored for Visium HD spatial transcriptomics at single-cell resolution. We show that cell-type-specific SVGs identified by ctSVG include many new genes that do not overlap with sample-wide SVGs or cell-type marker genes and that these genes reveal important biological functions in real spatial datasets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-025-03870-6.
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Zhuang, Haotian, Xinyi Shang, Wenpin Hou and Zhicheng Ji (2025). Identifying cell-type-specific spatially variable genes with ctSVG. Genome biology, 26(1). p. 416. 10.1186/s13059-025-03870-6 Retrieved from https://hdl.handle.net/10161/33781.
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