ArticleResearch square2024
Identifying cell-type-specific spatially variable genes with ctSVG.
Article in Research square, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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4 authors.
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Abstract
Spatially variable genes (SVGs) reveal the molecular and functional heterogeneity of cells across different spatial regions of a tissue. We found that sample-wide SVGs, identified by previous methods across the whole sample, largely overlap with cell-type marker genes derived from single-cell gene expression, leaving the spatial location information largely underutilized. We developed ctSVG, a computational method specifically tailored for Visium HD spatial transcriptomics at single-cell resolution. ctSVG accurately assigns Visium squares to cells and identifies cell-type-specific SVGs. 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.
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