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Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures | |
2020-01 | |
Source Publication | BRIEFINGS IN BIOINFORMATICS
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ISSN | 1467-5463 |
EISSN | 1477-4054 |
Volume | 21Issue:1Pages:248-261 |
Status | 已发表 |
DOI | 10.1093/bib/bby093 |
Abstract | Motivation: Estimating differentiation potency of single cells is a task of great biological and clinical significance, as it may allow identification of normal and cancer stem cell phenotypes. However, very few single-cell potency models have been proposed, and their robustness and reliability across independent studies have not yet been fully assessed. Results: Using nine independent single-cell RNA-Seq experiments, we here compare four different single-cell potency models to each other, in their ability to discriminate cells that ought to differ in terms of differentiation potency. Two of the potency models approximate potency via network entropy measures that integrate the single-cell RNA-Seq profile of a cell with a protein interaction network. The comparison between the four models reveals that integration of RNA-Seq data with a protein interaction network dramatically improves the robustness and reliability of single-cell potency estimates. We demonstrate that underlying this robustness is a correlation relationship, according to which high differentiation potency is positively associated with overexpression of network hubs. We further show that overexpressed network hubs are strongly enriched for ribosomal mitochondrial proteins, suggesting that their mRNA levels may provide a universal marker of a cell's potency. Thus, this study provides novel systems-biological insight into cellular potency and may provide a foundation for improved models of differentiation potency with far-reaching implications for the discovery of novel stem cell or progenitor cell phenotypes. |
Keyword | single-cell RNA-Seq entropy differentiation potency network Waddington |
URL | 查看原文 |
Indexed By | SCIE |
Language | 英语 |
WOS Research Area | Biochemistry & Molecular Biology ; Mathematical & Computational Biology |
WOS Subject | Biochemical Research Methods ; Mathematical & Computational Biology |
WOS ID | WOS:000516610800019 |
Publisher | OXFORD UNIV PRESS |
Original Document Type | Article |
Citation statistics | |
Document Type | 期刊论文 |
Identifier | https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/243343 |
Collection | 生命科学与技术学院 生命科学与技术学院_特聘教授组_陈洛南组 |
Corresponding Author | Teschendorff, Andrew E.; Chen, Luonan; Li, Tiejun |
Affiliation | 1.Peking Univ, Sch Math Sci, Beijing 100871, Peoples R China; 2.CAS MPG Partner Inst Computat Biol, Shanghai, Peoples R China; 3.UCL, London, England; 4.Chinese Acad Sci, Key Lab Syst Biol, Shanghai, Peoples R China; 5.Shanghai Inst Biol Sci, Shanghai, Peoples R China 6.School of Life Science and Technology, ShanghaiTech University, Shanghai 20121 |
Corresponding Author Affilication | School of Life Science and Technology |
Recommended Citation GB/T 7714 | Shi, Jifan,Teschendorff, Andrew E.,Chen, Weiyan,et al. Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures[J]. BRIEFINGS IN BIOINFORMATICS,2020,21(1):248-261. |
APA | Shi, Jifan,Teschendorff, Andrew E.,Chen, Weiyan,Chen, Luonan,&Li, Tiejun.(2020).Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures.BRIEFINGS IN BIOINFORMATICS,21(1),248-261. |
MLA | Shi, Jifan,et al."Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures".BRIEFINGS IN BIOINFORMATICS 21.1(2020):248-261. |
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