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| SPECIAL TOPIC — A celebration of the 90th Anniversary of the Birth of Bolin Hao |
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Analysis of spatiotemporal dynamic patterns of gene expression during mouse embryonic development based on Moran's I and spatial transcriptomics |
| Qi-Chao Li(李啟超)1,2,†, Hai Lin(林海)2,†, Peng Wang(王鹏)1,2, Qiutong Dong(董秋彤)1,2, Kun Wang(王坤)1,2, Jian-Wei Shuai(帅建伟)2,‡, and Fang-Fu Ye(叶方富)1,2,,§ |
1 Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou 325035, China;
2 Oujiang Laboratory (Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China |
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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.
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Received: 04 May 2025
Revised: 04 June 2025
Accepted manuscript online: 13 June 2025
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PACS:
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87.10.Vg
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(Biological information)
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87.85.mg
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(Genomics)
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05.45.Tp
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(Time series analysis)
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| Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 12090052, U24A2014, and 12325405). |
Corresponding Authors:
Jian-Wei Shuai, Fang-Fu Ye
E-mail: jianweishuai@xmu.edu.cn;fye@iphy.ac.cn
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Cite this article:
Qi-Chao Li(李啟超), Hai Lin(林海), Peng Wang(王鹏), Qiutong Dong(董秋彤), Kun Wang(王坤), Jian-Wei Shuai(帅建伟), and Fang-Fu Ye(叶方富) Analysis of spatiotemporal dynamic patterns of gene expression during mouse embryonic development based on Moran's I and spatial transcriptomics 2025 Chin. Phys. B 34 088703
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