Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data

Understanding the cellular microenvironment promises to deliver insights into disease and development, yet we still lack the ability to systematically leverage high resolution spatial transcriptomics to understand cell-cell interactions. With the aim of identifying cell-contact dependent genes, we propose a novel approach that explores the transcriptome of spatial beads composed of multiple cell types (heterotypic beads). Our approach identifies cell-contact dependent expression beyond what ligand-receptor co-expression can identify. ### Competing Interest Statement The authors have declared no competing interest.