SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

Advancements in spatial omics technologies have enabled the measurement of expression profiles of different molecules, such as genes (using spatial transcriptomics), and peptides, lipids, or N-glycans (using mass spectrometry imaging), across thousands of spatial locations within a tissue. While identifying molecules with spatially variable expression is a well-studied statistical problem, robust methodologies for detecting spatially varying co-expression between molecule pairs remain limited. To address this gap, we introduce a Bayesian fused modeling framework for estimating molecular co-expression at both local (location-specific) and global (tissue-wide) levels, offering a refined understanding of cell-cell communication (CCC) mediated through ligand-receptor and other molecular interactions. Through extensive simulations, we demonstrate that our approach, termed SpaceBF, achieves superior specificity and precision compared to existing methods that predominantly rely on geospatial metrics such as bivariate Moran's I and Lee's L. Applying our framework to real spatial transcriptomics datasets, we uncover novel biological insights into CCC patterns across different cancer types.