Cross-expression meta-analysis of 695 brain samples reveals coordinated gene expression across spatially adjacent cells.

ABSTRACT: Spatial transcriptomics promises to transform our understanding of tissue biology by molecularly profiling individual cells in situ. A fundamental question they allow us to ask is how nearby cells orchestrate their gene expression. Rather than focus on how these cells (samples) communicate with each other, we reframe the problem to investigate how genes (features) coordinate their expression between neighboring cells. To study these phenomena - called cross-expression - we compare all genes to find pairs that coordinate their expression between adjacent cells, thereby avoiding curating gene lists or annotating cell types. Our end-to-end method recovers ligand-receptor pairs as cross-expressing genes and finds gene combinations that mark anatomical regions, complementing marker gene-

SUBMITTER: Sarwar A 

PROVIDER: S-EPMC11429685 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature