PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics

PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics

18 January 2024 | Yuchen Liang, Guowei Shi, Runlin Cai, Yuchen Yuan, Ziying Xie, Long Yu, Yingjian Huang, Qian Shi, Lizhe Wang, Jun Li, Zhonghui Tang
The study introduces PROST, a framework for quantitative recognition of spatial transcriptomic patterns, consisting of two main components: the PROST Index (PI) and the PROST Neural Network (PNN). PI characterizes spatial variations in gene expression patterns through a novel index, while PNN uses a self-attention mechanism to cluster spatial domains. PROST demonstrates superior performance in identifying spatially variable genes (SVGs) and segmenting spatial domains across various spatial resolutions, from multicellular to cellular levels. The PROST Index can prioritize spatial expression variations, facilitating biological insights. The framework is validated on datasets from different platforms and resolutions, showing robustness and adaptability. PROST's ability to integrate spatial information and gene expression profiles makes it a flexible and powerful tool for analyzing spatial transcriptomic data.The study introduces PROST, a framework for quantitative recognition of spatial transcriptomic patterns, consisting of two main components: the PROST Index (PI) and the PROST Neural Network (PNN). PI characterizes spatial variations in gene expression patterns through a novel index, while PNN uses a self-attention mechanism to cluster spatial domains. PROST demonstrates superior performance in identifying spatially variable genes (SVGs) and segmenting spatial domains across various spatial resolutions, from multicellular to cellular levels. The PROST Index can prioritize spatial expression variations, facilitating biological insights. The framework is validated on datasets from different platforms and resolutions, showing robustness and adaptability. PROST's ability to integrate spatial information and gene expression profiles makes it a flexible and powerful tool for analyzing spatial transcriptomic data.
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[slides] PROST%3A quantitative identification of spatially variable genes and domain detection in spatial transcriptomics | StudySpace