SpaFun: discovering domain-specific spatial expression patterns and new disease-relevant genes using functional principal component analysis.

SpaFun is a novel, non-model-based method developed to address limitations in existing spatially variable gene detection techniques, particularly for large-scale spatially resolved transcriptomics datasets. These limitations include computational inefficiency, limited statistical power with increasing data size, and the inability to capture spatial heterogeneity and co-expression patterns among genes. Built on functional principal component analysis, SpaFun identifies domain-representative genes with significantly better computational efficiency and greater statistical power while accounting for spatial heterogeneity and co-expression patterns among genes. We applied SpaFun to three spatially resolved transcriptomics datasets and demonstrated that SpaFun outperformed state-of-the-art algorithms for identifying representative genes for tumor regions (e.g. DESeq, edgeR, and limma), as well as recently developed novel algorithms designed for spatial omics to identify the representative genes (e.g. SPARK and CSIDE). This highlights SpaFun's ability to accurately identify genes most representative of each spatial domain (e.g. tumor, immune, or stroma regions). By uncovering novel disease-relevant genes overlooked by existing algorithms, SpaFun could provide insights into new molecular mechanisms and propose innovative therapeutic strategies to improve patient outcomes.