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

ABSTRACT: Computational methods have been proposed to leverage spatially resolved transcriptomic data, pinpointing genes with spatial expression patterns and delineating tissue domains. However, existing approaches fall short in uniformly quantifying spatially variable genes (SVGs). Moreover, from a methodological viewpoint, while SVGs are naturally associated with depicting spatial domains, they are technically dissociated in most methods. Here, we present a framework (PROST) for the quantitative recognition of spatial transcriptomic patterns, consisting of (i) quantitatively characterizing spatial variations in gene expression patterns through the PROST Index; and (ii) unsupervised clustering of spatial domains via a self-attention mechanism. We demonstrate that PROST performs superior SVG identif

SUBMITTER: Liang Y 

PROVIDER: S-EPMC10796707 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature