Our study introduces scITDG,a tool designed for the analysis of time-dependent gene expression in single-cell transcriptomic sequencing data,effectively filling a gap in current analytical resources.A key advantage of...Our study introduces scITDG,a tool designed for the analysis of time-dependent gene expression in single-cell transcriptomic sequencing data,effectively filling a gap in current analytical resources.A key advantage of scITDG is its ability to identify dynamic gene expression patterns across multiple time points at single-cell resolution,which is pivotal for deciphering com-plex biological processes such as aging and tissue regeneration.The tool is compatible with widely used single-cell analysis platforms such as Seurat and Scanpy.By integrating natural cubic splines regression with bootstrapping resampling,scITDG enhances the functionality of these platforms and broadens their applicability.In this study,based on scITDG,we revealed intricate gene expression modules in mice aging and axolotl limb regeneration,providing valuable insights into cellular function and response mechanisms.The versatility of scITDG makes it applicable to a wide range of biological contexts,including development,circadian rhythms,disease progression,and therapeutic responses.展开更多
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDC0200000)the National Natural Science Foundation of China(82322025,82488301,82125011,82271600,82361148131)+15 种基金the National Key Research and Development Pro-gram of China(2022YFA1103700,2020YFA0804000)the Stra-tegic Priority Research Program of the Chinese Academy of Sci-ences(XDA0460403)the National Natural Science Foundation of China(92168201,82330044,32341001,32121001,82192863,82361148130,8231101626)Non-Communicable Chronic Diseases-National Science and Technology Major Project(2024ZD0530400)Youth Innovation Promotion Association of CAS(2022083)Young Elite Scientists Sponsorship Program by CAST(2021QNRC001)International Partnership Program of Chinese Academy of Sciences(073GJHZ2023019FN)he Program of the Beijing Natural Science Foundation(JQ24044,Z240018,F251011,Z230011)Shenzhen Medi-cal Research Fund(C2406001)CAS Project for Young Scientists in Basic Research(YSBR-076,YSBR-012)the Informatization Plan of Chinese Academy of Sciences(CAS-WX2022SDC-XK14)New Cor-nerstone Science Foundation through the XPLORER PRIZE(2021-1045)Beijing Municipal Public Welfare Development and Reform Pilot Project for Medical Research Institutes(JYY2023-13)CAS Youth Interdisciplinary Team,Key Laboratory of Alzheimer's Disease of Zhejiang Province(ZJAD-2024001)Initiative Scientific Research Program,Institute of Zoology,CAS(2023IOZ0102,2023IOZ0202,2024IOZ0103)Beijing Anzhen Hospital High Level Research Funding(2024AZB3002).
文摘Our study introduces scITDG,a tool designed for the analysis of time-dependent gene expression in single-cell transcriptomic sequencing data,effectively filling a gap in current analytical resources.A key advantage of scITDG is its ability to identify dynamic gene expression patterns across multiple time points at single-cell resolution,which is pivotal for deciphering com-plex biological processes such as aging and tissue regeneration.The tool is compatible with widely used single-cell analysis platforms such as Seurat and Scanpy.By integrating natural cubic splines regression with bootstrapping resampling,scITDG enhances the functionality of these platforms and broadens their applicability.In this study,based on scITDG,we revealed intricate gene expression modules in mice aging and axolotl limb regeneration,providing valuable insights into cellular function and response mechanisms.The versatility of scITDG makes it applicable to a wide range of biological contexts,including development,circadian rhythms,disease progression,and therapeutic responses.
