CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data.

ABSTRACT: Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and receptors, cells use diverse channels including gap junctions to communicate with their immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach to investigate cell neighbor-dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize cells based on their microenvironment, CellNeighborEX uses direct cell location or the mixture of transcriptome from multiple cells depending on ST technologies. For each cell type, CellNeighborEX identifies diverse gene sets associated with partnering cell types, providing fu

SUBMITTER: Kim H 

PROVIDER: S-EPMC10632736 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature