Cell Modeling and Simulation

Yachie‐Kinoshita, Ayako; Kaizu, Kazunari

doi:10.1016/b978-0-12-809633-8.20294-x

Cited by 1 publication

(1 citation statement)

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“…The GRN represents a complex web of interactions between genetic materials including transcription factors (TFs) and downstream genes across different cell types and developmental stages. Although the GRN orchestrates cell functions via intracellular signaling within a cell, it is profoundly influenced by extracellular communications from neighboring cells in the spatial context 3,4 . For instance, the determination of distinct mesodermal cell fates in sea urchin embryonic development is driven by the spatially confined activation of the mesoderm GRN, which is restricted by the proximal endoderm cells 5 .…”

Section: Introductionmentioning

confidence: 99%

SpaGRN: investigating spatially informed regulatory paths for spatially resolved transcriptomics data

Li,

Liu,

Guo

et al. 2023

Preprint

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SUMMARYCells expressing similar transcriptional regulatory circuits spatially aggregate into distinct cell types or states. However, most existing methods for inferring gene regulatory networks from spatially resolved transcriptomics are devoted to spatial co-expression modules or interactions between transcription factors and target genes, neglecting mediated effects from extracellular signals. Here we introduce SpaGRN, a statistical framework for predicting the comprehensive intracellular regulatory network underlying spatial patterns by integrating spatial expression profiles with prior knowledge on regulatory relationships and signaling paths. We validate and assess SpaGRN using simulated and real datasets, demonstrating its efficiency, performance, and robustness. When applied to 3D datasets of developingDrosophilaembryos and larvae, SpaGRN identifies spatiotemporal variations in specific regulatory patterns, delineating the cascade of events from receptor stimulation to downstream transcription factors and targets, revealing synergetic regulation mechanism during organogenesis. Moreover, SpaGRN provides flexible visualization functions. We construct an online 3D regulatory network atlas database for interactive exploration and sharing.

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Section: Introductionmentioning

confidence: 99%