Analysis of spatiotemporal dynamic patterns of gene expression during mouse embryonic development based on Moran’s I and spatial transcriptomics

Abstract Spatial transcriptomics technology provides novel insights into the spatial organization of gene expression during embryonic development. In this study, we propose a method that integrates analysis across both temporal and spatial dimensions to investigate spatial transcriptomics data from mouse embryos at different developmental stages. We quantified the spatial expression pattern of each gene at various stages by calculating its Moran’s I. Furthermore, by employing time-series clustering to identify dynamic co-expression modules, we identified several developmentally stage-specific regulatory gene modules. A key finding was the presence of distinct, stage-specific gene network modules across different developmental periods: Early modules focused on morphogenesis, mid-stage on organ development, and late-stage on neural and tissue maturation. Functional enrichment analysis further confirmed the core biological functions of each module. The dynamic, spatially-resolved gene expression model constructed in this study not only provides new biological insights into the programmed spatiotemporal reorganization of gene regulatory networks during embryonic development but also presents an effective approach for analyzing complex spatiotemporal omics data. This work provides a new perspective for understanding developmental biology, regenerative medicine, and related fields.