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redpath:Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer

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Genomics, Proteomics & Bioinformatics 2021年第2期19卷 292-305页

作者： Kaikun Xie Zehua Liu Ning Chen Ting Chen Institute for Artificial Intelligence State Key Lab of Intelligent Technology and SystemsDepartment of Computer Science and TechnologyTsinghua UniversityBeijing 100084China Tsinghua-Fuzhou Institute of Digital Technology Beijing National Research Center for Information Science and TechnologyTsinghua UniversityBeijing 100084China Center for Computational and Integrative Biology Massachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA Department of Molecular Biology Massachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA Broad Institute of Massachusetts Institute of Technology and Harvard CambridgeMA 02142USA

The recent advancement of single-cell RNA sequencing(scRNA-seq)technologies facilitates the study of cell lineages in developmental processes and *** this study,we developed a computational method,called redpath,to reconstruct the pseudo developmental time of cell lineages using a consensus asymmetric hamiltonian path ***,we developed a novel approach to visualize the trajectory development and implemented visualization methods to provide biological *** validated the performance of redpath by segmenting different stages of cell development on multiple neural stem cell and cancer datasets,as well as other single-cell transcriptome *** particular,we identified a stem cell-like subpopulation in malignant glioma *** cells express known proliferative markers,such as GFAP,ATP1A2,IGFBPL1,and ALDOC,and remain silenced for quiescent markers such as ***,we identified MCL1 as a significant gene that regulates cell apoptosis and CSF1R for reprogramming macrophages to control tumor *** conclusion,redpath is a comprehensive tool for analyzing scRNA-seq datasets along the pseudo developmental *** is available at https://***/tinglabs/redpath.

关键词： Single-cell pseudotime reconstruction consensus hamiltonian path Cell differentiation Cell proliferation Cell development and diseases

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