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

作     者：Kaikun Xie Zehua Liu Ning Chen Ting Chen Kaikun Xie;Zehua Liu;Ning Chen;Ting Chen

作者机构：Institute for Artificial IntelligenceState Key Lab of Intelligent Technology and SystemsDepartment of Computer Science and TechnologyTsinghua UniversityBeijing 100084China Tsinghua-Fuzhou Institute of Digital TechnologyBeijing National Research Center for Information Science and TechnologyTsinghua UniversityBeijing 100084China Center for Computational and Integrative BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA Department of Molecular BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMA 02142USA 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2021年第19卷第2期

页      面：292-305页

核心收录：

学科分类：0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 07[理学] 08[工学] 

基　　金：the National Natural Science Foundation of China(Grant Nos.61872218,61721003,61673241,and 61906105) the National Key R&D Program of China(Grant No.2019YFB1404804) the Beijing National Research Center for Information Science and Technology(BNRist),China the Tsinghua University-Peking Union Medical College Hospital Initiative Scientific Research Program,China 

主　　题：Single-cell pseudotime reconstruction Consensus Hamiltonian path Cell differentiation Cell proliferation Cell development and diseases 

摘      要：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.