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bioRxiv · 10.64898/2026.04.20.719761

High Purity Differential Expression of Genes across Spatial Domains

Wang, B.·Guo, C.·He, J.·Gao, L.
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Abstract

Spatial transcriptomics maps gene expression within tissue architecture, offering deep insights into cellular function. A key yet overlooked phenomenon is the systematic imbalance in gene regulation within spatial domains, contrasting with traditional analyses. We define and validate this as a prevalent hallmark--High-Purity Differential Expression (HiP-DEP)--where genes in a domain shift predominantly in one direction (i.e., predominantly up- or downregulated). We introduce a Spatial Purity index to quantify it. Analysis of 190 diverse datasets across diverse tissues, diseases, and technologies revealed that spatial domains possess significantly higher purity than conventional bulk (p = 5.4 x 10-11) or single-cell data (p = 6.9 x 10-14), establishing HiP- DEP as a core hallmark of spatial biology. Using our HiP-DEP framework, we show its utility in: decoding core oncogenic regulation and its spatial gradient in breast cancer; uncovering hidden phenotypic divergence between morphologically similar Alzheimers plaques; and identifying active cellular communication niches in normal brain tissue. By shifting focus from individual genes to coordinated transcriptional programs, HiP-DEP provides a new paradigm for precision spatial omics analysis.

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Wang, B., Guo, C., He, J., Gao, L.. 2026-04-23. High Purity Differential Expression of Genes across Spatial Domains. https://doi.org/10.64898/2026.04.20.719761

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