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

The recent advancement of single-cell RNA sequencing (scRNA-seq) technologies facilitates the study of cell lineages in developmental processes and cancer. In this study, we developed a computational method, called redPATH, to reconstruct the pseudo developmental time of cell lineages using a consen...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Kaikun Xie, Zehua Liu, Ning Chen, Ting Chen
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Single-cell pseudotime reconstruction Consensus Hamiltonian path Cell differentiation Cell proliferation Cell development and diseases Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/84f6976d27554d73bf95a2ea2bef2873
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:84f6976d27554d73bf95a2ea2bef2873
record_format	dspace
spelling	oai:doaj.org-article:84f6976d27554d73bf95a2ea2bef28732021-11-16T04:09:22ZredPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer1672-022910.1016/j.gpb.2020.06.014https://doaj.org/article/84f6976d27554d73bf95a2ea2bef28732021-04-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S167202292100019Xhttps://doaj.org/toc/1672-0229The recent advancement of single-cell RNA sequencing (scRNA-seq) technologies facilitates the study of cell lineages in developmental processes and cancer. In this study, we developed a computational method, called redPATH, to reconstruct the pseudo developmental time of cell lineages using a consensus asymmetric Hamiltonian path algorithm. Besides, we developed a novel approach to visualize the trajectory development and implemented visualization methods to provide biological insights. We 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 data. In particular, we identified a stem cell-like subpopulation in malignant glioma cells. These cells express known proliferative markers, such as GFAP, ATP1A2, IGFBPL1, and ALDOC, and remain silenced for quiescent markers such as ID3. Furthermore, we identified MCL1 as a significant gene that regulates cell apoptosis and CSF1R for reprogramming macrophages to control tumor growth. In conclusion, redPATH is a comprehensive tool for analyzing scRNA-seq datasets along the pseudo developmental time. redPATH is available at https://github.com/tinglabs/redPATH.Kaikun XieZehua LiuNing ChenTing ChenElsevierarticleSingle-cell pseudotime reconstructionConsensus Hamiltonian pathCell differentiationCell proliferationCell development and diseasesBiology (General)QH301-705.5ENGenomics, Proteomics & Bioinformatics, Vol 19, Iss 2, Pp 292-305 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Single-cell pseudotime reconstruction Consensus Hamiltonian path Cell differentiation Cell proliferation Cell development and diseases Biology (General) QH301-705.5
spellingShingle	Single-cell pseudotime reconstruction Consensus Hamiltonian path Cell differentiation Cell proliferation Cell development and diseases Biology (General) QH301-705.5 Kaikun Xie Zehua Liu Ning Chen Ting Chen redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer
description	The recent advancement of single-cell RNA sequencing (scRNA-seq) technologies facilitates the study of cell lineages in developmental processes and cancer. In this study, we developed a computational method, called redPATH, to reconstruct the pseudo developmental time of cell lineages using a consensus asymmetric Hamiltonian path algorithm. Besides, we developed a novel approach to visualize the trajectory development and implemented visualization methods to provide biological insights. We 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 data. In particular, we identified a stem cell-like subpopulation in malignant glioma cells. These cells express known proliferative markers, such as GFAP, ATP1A2, IGFBPL1, and ALDOC, and remain silenced for quiescent markers such as ID3. Furthermore, we identified MCL1 as a significant gene that regulates cell apoptosis and CSF1R for reprogramming macrophages to control tumor growth. In conclusion, redPATH is a comprehensive tool for analyzing scRNA-seq datasets along the pseudo developmental time. redPATH is available at https://github.com/tinglabs/redPATH.
format	article
author	Kaikun Xie Zehua Liu Ning Chen Ting Chen
author_facet	Kaikun Xie Zehua Liu Ning Chen Ting Chen
author_sort	Kaikun Xie
title	redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer
title_short	redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer
title_full	redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer
title_fullStr	redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer
title_full_unstemmed	redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer
title_sort	redpath: reconstructing the pseudo development time of cell lineages in single-cell rna-seq data and applications in cancer
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/84f6976d27554d73bf95a2ea2bef2873
work_keys_str_mv	AT kaikunxie redpathreconstructingthepseudodevelopmenttimeofcelllineagesinsinglecellrnaseqdataandapplicationsincancer AT zehualiu redpathreconstructingthepseudodevelopmenttimeofcelllineagesinsinglecellrnaseqdataandapplicationsincancer AT ningchen redpathreconstructingthepseudodevelopmenttimeofcelllineagesinsinglecellrnaseqdataandapplicationsincancer AT tingchen redpathreconstructingthepseudodevelopmenttimeofcelllineagesinsinglecellrnaseqdataandapplicationsincancer
_version_	1718426735492464640

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

Ejemplares similares